My biggest complaint is Sense. It's far better than Blur, in my opinion, and even better than I expected it to be, but there are just a few quirks about it that HTC messed up that bother me (e.g., the messaging notification sound set via Personalize doesn't actually work, the browser only lets me open 4 or 5 windows, the main Messages text box is set up wrong so Swype can't auto-space...)
I came from an LG Ally which, though it was a low-end smartphone, came with near-stock Android. It had an LG launcher, but it also came with the stock Android launcher, and they didn't go out of their way to dink with all the included apps, and I liked it that way.
I know there are third-party replacements, but I think Google's done a great job. Though I understand the need to create a brand presence, I feel like these full system "skins" (which are really just full replacements of apps) are a little silly at times.
I make it sound worse than it is, but I'll definitely be trying more AOSP-ish ROMs when they come out.