Only can comment on my '07 Ultra:
1) Gearing on the 6 speed is too tall and drive train makes a lot more noise than my '04 Wide Glide did. The gearing may be related to a few things: horsepower, bike being heavy, etc.
2) The stock seat is terrible compared to say a Mustang
3) I think the chain driven cams and tensioners is a poor design, especially when they have to be inspected/replaced at 40K, which is about a $600 bill. Cams should be something you never have to think about until engine rebuild time.
4) Air temp guage should be replaced with an oil temp guage
5) Fried thighs - better exhaust routing would be nice
Other than those gripes, I'm happy with the bike. I was surprised than the 96 doesn't seem that much more powerful than my old 88, but then again my Wide Glide was about 200 pounds lighter. I didn't buy the bike for speed so it's fine for me. I do like that I can run at 80 without the motor screaming - that's the only part of the 6 speed I like.