I've had an 07 and 09 CVO SE Ultra. My 07 had cylinder leaks at about 6k, my 09 had a clacking noise from day one that I finally got fixed at an out of town dealer (100+ miles away) right before I traded it. I went with a stock 96 ultra in 2010, upgraded to a 103. That one had some issues as well, but most self inflicted.
I now have a 2011 FLTRUSE road glide and it has been in the shop for the following:
1. clutch seals leaking fluid onto clutch handle, seals replaced.
2. replacement seals didn't work, so clutch cylinder was replaced.
3. upon replacement of clutch master cylinder, dealer noticed clear coat had been affected by brake fluid that blew on it while riding.
4. fixed aforementioned paint problems.
5. upon receipt of bike, noticed CD door cover was hanging slightly. Door was broken on a clip or two; radio needed to be replaced.
6. replaced radio.
7. upon receipt and first ride, noticed the key fob nor dash switch would lock the locks. Also ignition switch was very hard to turn all the way to the "lock" (far left) position (this was from day on however).
8. returned to have locking mechanism fixed.
9. upon receipt, first ride right blinker stuck to solid on along with the right front and right rear bulb. Also, red key icon on dash came and stayed on.
10. returned to fix. Just got it back today.
Hopefully that will be it. I think the problems after the clutch repair were self inflicted by a tech or two so can't say that was faulty harware.
The only challenge I have with this bike is the heat I STILL experience after installing a TTS fuel management system and fullsac baffles (both exceptional product btw). Personally, I think with all the changes HD has had to make regarding EPA regulations, the ECM 9brain box) will only allow you to tune it so far. I think once you have ridden the bike after a tune (changes to AFR, making it richer to cool) it brings it back to a default rnage of at or near stoich (14.7) which burns the piss out of my right lower leg in the summer time.
Other than that....this is the most comfortable bike I have owned to date including a lot more than the ones mentioned above.
I think a lot (if not most) of the problems we have with our bikes are self inflicted. Harley spends a lot of money on R&D to get these bikes right. Once we start changing things, the ripple effect sets in. I've seen a few folks on here that go 10's of thousands of miles with zero problems and they run stock.