Here's some to add.
The rear bearing becomes loose in the wheel. Which leads to having to replace the hub at around $600.00 or buy another rim used or a new rim made by someone other then yamaha!

Starter solenoid going out. Leaving you stranded in another state 1000's of miles from home.

But like others have said I still like my R* and I know that no matter what brand of bike you ride they all have their share of problems. That is why I get upset when people put other bikes(harley) down. Our R*'s are not perfect either.

Even though I have experianced the trans recall, the clutch slippage, the starter solenoid problem, the rear wheel bearing coming loose, the tank not venting causing my tank to literally get sucked in and dented, I would not hesitate to jump on either one of my R*'s and ride anywhere, But then again I will jump on my harley with that same confidence and just ride and smile and if a problem occurs I have a cell phone and my debt. card.

That makes me feel better since mine is a 99.............

Hows this.
2 years ago while riding down to Fl. I meet a guy in South Carolina who was riding a 99 Star.
He was on his way back to South Bend Indiana.
He told me he bought his bike brand new, averaged over 20,000 miles a year and had road it to every state except Hawaii(sp).