Top 3 things you DON'T like about the FJ

[rodan]

I've only had mine for a couple of days and around 150 miles, but have a couple minor nits to pick...
 
I would have preferred an analog tach... LCD bars are too hard to read when you're wicking it up.
 
It should have come with cruise control.
 
I would gladly have paid more $$ for fully adjustable suspension. I don't know why the Japanese refuse to put good suspension on anything but sportbikes.

[hawkgt]

Stock shield is better than my V-Strom, but not much, Madstad set-up is on my to-do list. Hand guards are more style over function, too thin and too far away to block much wind, aftermarket will probably give us some options in the near future. Suspension is okay once you set the sag and tune it to your weight and preference, but it's definitely a price point component.

[Guest lawrenceofsuburbia]

Stock seat.
Suspension.
Spiky footpegs that prevent me from easily/ comfortably moving my feet around on the pegs - unnecessary on a purely road bike.
L of S

[korben]

Actually the first two are more my problems than the bikes but..
 
I have big feet which makes getting the side stand down not easy.
I have big feet that when I have the balls of my feet on the foot pegs the rear are resting on the rear pegs.
They didn't do a white one!!

[jimf]

I have big feet which makes getting the side stand down not easy.

I had a lot of problems with getting the sidestand down until I removed the (gigantic) peg feeler; the feeler would keep knocking my toe off the sidestand tab.  It drove me nuts.  Without it I can extend it cleanly every time. 
Of course the downside to removing the peg feeler is that the centerstand becomes your feeler.  I can live with that, both because I don't live in an area where the roads make that a common occurrence and because, even if I did, I'd still be extending the sidestand a lot more than rubbing hard parts in corners.
 
(Plus beveling your centerstand could be considered hero marks.  I have a friend who's thinking of selling his nicely-rounded-off centerstand from a Ducati Multistrada to some poseur.  Ahh, entrepreneurship.)
 
 

[korben]

I have big feet which makes getting the side stand down not easy.

I had a lot of problems with getting the sidestand down until I removed the (gigantic) peg feeler; the feeler would keep knocking my toe off the sidestand tab.  It drove me nuts.  Without it I can extend it cleanly every time. 
Of course the downside to removing the peg feeler is that the centerstand becomes your feeler.  I can live with that, both because I don't live in an area where the roads make that a common occurrence and because, even if I did, I'd still be extending the sidestand a lot more than rubbing hard parts in corners.
 
(Plus beveling your centerstand could be considered hero marks.  I have a friend who's thinking of selling his nicely-rounded-off centerstand from a Ducati Multistrada to some poseur.  Ahh, entrepreneurship.)
 

The feeler is the only part I can get my foot to.  Without that I'd have to climb off the bike first to put the stand down. 

[jimf]

I'm thinking about getting an FJ, but I like to do my research.  What are your concerns?  Windshields?  Mileage?  Maintenance?  Seat?

My primary concern was the windscreen.  The stocker is really loud.  I mean, *really* loud, even through earplugs.  By far the worst of any bike I've ever ridden. 
There are a number of windscreen replacements, both larger and smaller, and by all reports they're all better.  The downside to replacements is that there is often interference with the handguards to some degree in some or all windshield height levels.  For instance, the two Ermax screens I've purchased interfere at the highest setting, although cutouts mean full turn range at medium and low settings.  Some screens have interference no matter what the setting.
 
For my money the Ermax sport is the best of the windshields I've used -- it pulls the wind off my chest but leaves my helmet in clean air.  I also have their touring screen which has far more coverage and is better as a result in cold or wet weather, and works perfectly up to around 60mph, but it's still fairly loud at highway speeds.  That likely wouldn't be the case if you're a taller rider.  I'm only 5'4" and if I stand up slightly things get much quieter with that screen, so I'm sure it will work well for other riders.
 
All of which is to say that YMMV with individual windshields, but for sure you can do much better than stock, and replacements aren't expensive ($95-105 for the Ermax screens I bought).
 
Some people don't like the seat but I found it firm enough for all-day usage, the 2nd best stock seat of any bike I've owned (admittedly only five of them, oddly the Daytona 675 being the best of the lot) and the 3rd of any I've ridden any distance (the Versys 650 I rented was better too).  My only complaint is that the seat is slightly squared off and after 6+ hours I started to notice the edge, but it wasn't a serious hot-spot.  I may eventually reupholster the seat and cut the edges down a bit when I do so, or replace it with something else, but I don't see an immediate need.
 
I could use some sort of cruise control or throttle lock for highway droning.  I don't do enough of that (BRP!) to be terribly annoyed, but once in awhile it's very nice to have.  Unfortunately the handguards preclude the use of something like a Throttle Meister, although it looks like the old o-ring trick should work and I'll be trying that eventually.  (Bonus: That means the throttle lock will cost about $.25, much better than the $150 or so my last Throttle Meister set me back.)
 
I've not had the wobble complaints that others have complained about.  That might be because I don't usually ride high speed, or because the suspension set up was pretty good for me out of the box, or whatever.  I've not seen any need yet for something like a steering stabilizer.
 
There are complaints about the suspension and I'll echo them to a degree -- it's not great suspension, although it's the best out-of-the-box suspension I've had on four different Japanese bikes.  My only complaint so far is that the compression damping is a bit harsh.  Rebound seems adequate.  Spring rates are soft for a 200lb rider plus luggage but not bad for me without luggage.  I'll surely upgrade suspension as the bike ages but it's good enough for now.  Of course, I am not racing the thing or riding it near the limits, where suspension shortcomings would become much more obvious.
 
Low-rpm fueling can be a bit spastic, although in STD mode I find it similar to a number of other fuel-injected bikes I've owned and ridden.  "B" throttle mode is very smooth, very carb-like, so in situations where throttle control is difficult I just switch to that.
 
Beyond these things I found the FJ very nice out of the box.  The riding position is terrific, the motor is wonderful, it's pretty light, the handling is superb.  A very nice base platform.
 
Oh, there is one more thing.  The bike is proving so popular that Yamaha is backordered a couple of months for things like heated grips and hard luggage.  But good things come to those who wait :-).

[korben]

I know other's haven't appreciated the seat, but I've been ok with it. I can ride none stop from tank full to tank empty and a 2 minute break filling up the bike allows the short break I need. I rode for 8 hours last Saturday. Everything from country lanes, to very busy cities and a little motorway and had no complaints.
 
The stock screen is noisy, but on the lowest setting (I'm 5'10") I find the best... The noise is constant and the wind isn't buffeting so I'm happy.
 
I've had the front end wobble, but it's not bothering me too much... A slight reminder to keep it sensible!! I am considering a damper though as when I start adding luggage I suspect it'll get worse.

[rodan]

I have big feet which makes getting the side stand down not easy.

I had a lot of problems with getting the sidestand down until I removed the (gigantic) peg feeler; the feeler would keep knocking my toe off the sidestand tab.  It drove me nuts.  Without it I can extend it cleanly every time. 
Of course the downside to removing the peg feeler is that the centerstand becomes your feeler.  I can live with that, both because I don't live in an area where the roads make that a common occurrence and because, even if I did, I'd still be extending the sidestand a lot more than rubbing hard parts in corners.
 
(Plus beveling your centerstand could be considered hero marks.  I have a friend who's thinking of selling his nicely-rounded-off centerstand from a Ducati Multistrada to some poseur.  Ahh, entrepreneurship.)
 

Be careful....
 
I bought a 2002 VStrom 1k when they first came out, and the centerstand was a Suzuki accessory.  When I installed mine, it came with a ridiculously long feeler for the left side peg, so I left it off.  I took the bike to a trackday sometime later and grounded the centerstand, levering the rear wheel off the ground.  This resulted in a huge slide, near highside, and a much elevated heartrate!  When I got home, I put the long feeler back on immediately!  Trust me that you don't want to ground your centerstand... I was very lucky not to crash.  Stock pegs pivot when they touch down, the centerstand won't.
 
I do agree the feeler is in the way of the kickstand, though.  I figure I will get used to the 'proper technique' with time.
 

[dooder]

I hate that new bike smell mine came with, and the sense of fear that I have over where the first scratch is going to come from. What I really hate is how many freaking angles and small shiny bits the bike has. I got caught in the rain the other day riding, black and red with road splash looks awful. 20 minute ride took me an hour to clean up. In all seriousness, my only complaint is that I come from soft suspensioned, soft throttled dual sport bikes. The FJ has a wicked snap to the throttle I still have to be careful of, and the suspension is stiff enough that I feel it rolling over earthworms. So far, I'm loving it. Come back in a year and ask me again.

[wessie]

I hate that new bike smell mine came with, and the sense of fear that I have over where the first scratch is going to come from. What I really hate is how many freaking angles and small shiny bits the bike has. I got caught in the rain the other day riding, black and red with road splash looks awful. 20 minute ride took me an hour to clean up. In all seriousness, my only complaint is that I come from soft suspensioned, soft throttled dual sport bikes. The FJ has a wicked snap to the throttle I still have to be careful of, and the suspension is stiff enough that I feel it rolling over earthworms. So far, I'm loving it. Come back in a year and ask me again.

Just don't wash it. After 600 miles the muck doesn't get any thicker. In addition, scratches are invisible.
 
I've ridden nearly 2000 miles now and my bike has a patina that really gets attention.  

[skipperT]

I've only got one annoyance:
 
On the RH footrest you can rest your heel on the foot rest guard (which prevents your heel from hitting the exhaust pipe) but no such luck on the LH side.
 
I find my LH heel bouncing with the swingarm movement if I have both feet in the same position on the footrests.
 
Yeah it's weird that I notice these things. 8-)
 
-skip

[vespadaddy]

I've only got one annoyance:  
On the RH footrest you can rest your heel on the foot rest guard (which prevents your heel from hitting the exhaust pipe) but no such luck on the LH side.
 
I find my LH heel bouncing with the swingarm movement if I have both feet in the same position on the footrests.
 
Yeah it's weird that I notice these things. 8-)
 
-skip

Agreed.  Much like my last new Yamaha, a 2003 R6, my left heel would eventually wear through the black satin finish on the swingarm.  I've been protecting it with a strip of clear packing tape, but will probably replace that with some sort of 3M clear paint protection vinyl. 
Speaking of vinyl, does anyone have tips on what to buy, and what not to buy for paint protection vinyl?  I intend to cover both headlights, and the adjacent painted front fairing bits that are next to the headlight.

[Guest branthopolis]

I've only got one annoyance:  
On the RH footrest you can rest your heel on the foot rest guard (which prevents your heel from hitting the exhaust pipe) but no such luck on the LH side.
 
I find my LH heel bouncing with the swingarm movement if I have both feet in the same position on the footrests.
 
Yeah it's weird that I notice these things. 8-)
 
-skip

I noticed this one on my first FJ ride...   Rolled over a speed bump..   Centerstand bumped the bottom of my foot..  I freaked out for a second or two..    

[panooch]

Lamin-X Protective Film has a listing for the FJ-09 headlamps. I have not used their products so I'm unable to comment on quality. But it looks like they may be precut for the headlamps. They also sell sheets for a cut to fit application on other areas.