Well, I've owned a 2007 model year for 9 months, here we go:
-Poor visibility when looking over your shoulder on the driver's side.
Kinda sorta problems
-Gas bladder is a pain, but it was rectified in newer model years. It doesn't actually affect anything important, it's more a "first world problem".
Hypermiling problems that would not affect normal people
-Very touchy traction control. Again, mostly irrelevant to actual operation, but when hypermiling it's annoying to lose so much regen just from going over a teeny bump in the road and having the car switch almost entirely to hydraulic braking.
-10 seconds of idling under 6 mph needed to switch to full hybrid operation. Probably the worst from a hypermiling standpoint. This has been fixed on the newer models.
I'll update this, but that's all I can think of.