On the regular Rockets many claim that the rear tires wear out fast (3000-5000 miles). Although I have a friend who got 11,000 on his rear tire and claims that the guys whose tires wear out are all 350 lbs and performing burnouts at every stop light. Many put car tires on their r3's ("going darkside")because the tires are cheaper and last longer but this is extremely controversial too and the pro/con arguments have a religious fervor about them.
There are clutch issues. I can vouch for this personally because my r3T is currently in the shop getting its clutch rebuilt. Triumph is covering the repair even though the bike is out of warranty. I think its cheaper for them to just cover the bikes when the clutches fail than to issue a recall (which many on the R3 owners forums have been calling them to do.)
The thing I like least about the Rocket is the amount of heat it generates. Trying to mitigate this is an ongoing mission of mine. I've tried loading different tunes, I recently put on a set of ceramic-coated headers - still hot. It's not a lot of fun to be stuck in traffic on a Rocket in summertime. I think the heat will extend my riding season into December though :-)
Your MPGs will go down. Budget an extra 20-25% for fuel. But your speed and acceleration will go up too so that kinda compensates for it.
The thing I like least about having a Rocket is that I now have to go to r3owners.com and r3owners.net to commiserate about my bike instead of bonnevilleamerica.com!
Net/net I'm bummed about the bike being down with the clutch rebuild but after some initial challenges getting used to it, I really like it. It's a head turner, it has a ton of character from a 'ride' standpoint, and there's something about knowing you can kick the @$$ of any Harley out there (no matter how obnoxiously loud their pipes are) that makes it worth every bit of big-bike aggravation.