I personally maintain the bike, so I would only mention problems with it that are NOT due to neglect.
1. The bike was designed with a sealed battery, and it is charged/maintained by its alternator/generator that has an internal voltage regulator. The voltage regulator eventually fails probably due to the heat and vibration from the engine. The result is the battery's short life from over charging. The battery basically, and eventually gets cooked. A $28 external adjustable voltage regulator mounted elsewhere cured the problem.
2. The clutch plates have a wire circlip installed among them. (Rumor has it that Yamaha used it to during assembly). The cir-clip has broke and took a chunk out of a clutch plate. I removed the circlip and replaced the plate. 30 minute job. With the bike on the side stand, you don't even need to drain the oil!
3. 'Whistling gas cap'. Rubber vent flaps in the gas cap eventually harden and restrict air flow to vent the tank. Remove the rubber flaps from the internals of the gas cap assembly. They're not needed. 20 minutes? I did this myself and I don't claim to be a tech by any means.
These 3 design flaws are the only ones I have encountered with the bike. The rest is preventable with regular maintenance.
Incredible bike all around! I have had some good bikes that lasted, but not like this one. The bike is so easy to work on! If I can maintain it properly, anyone can! The FJ platform is a gold mine as well for easy performance improvements. Different parts from newer bikes can be installed to increase horsepower and performance dramatically, if need be. Presently, I have no need to increase the performance or horsepower!
I haven't the guts to drag my knee, but I love to push it and have fun as best I can. It has tons of power for me! With just aftermarket 'cans' (the rest of the bike is stock), it can stay with, and drive by new 600RR's.
The bike is the ultimate tourer as well. It has the strength needed to carry my wife and I, and three large side and top cases, and be comfortable enough to drive across country.
What a fast, solid bike! The looks are there too!