I've had the Trophy for about 5 weeks now, overall I really like it but I too have a few issues.
Like others the capacitive buttons are a pain, I dislike the vibrate, I dislike hitting them when I don't want to and it would be nice to wake the phone from those buttons. The LG device was horrible, and I believe all the others are capacitive (at least partly).
The camera is poor, but I knew that's what you get with HTC.
The alarm clock is useless, although I'm not sure who is to blame here, HTC or Microsoft. It's too quiet and would never wake me, also if it's left to run more than once without being dismissed the phone crashes and needs a restart, should be a quick software fix. The marketplace app seems to crash occasionally too.
My disappointments are largely hardware related, it's a real shame there is no one making really great quality hardware (Zune HD/iPhone 4 like build & design with Sony Ericsson camera/lens). I hope this will change, but I fear not, the same is true for Android, I don't understand why no one gets this.
I don't have an issue with the app list, I think it works suprisingly well, a quick swipe and a tap to stop. I only have 30 extra apps installed so far but I find it quick to get to things.
I love the way the software feels, its fast & smooth and not full of candy buttons and gradients that 1995 wants back. The tiles are great, the people hub is great, email is great, IE is good, maps is great but I'd like to see birds eye view too. I love the hardware camera button to unlock and the swipe right to see photos, Zune is great so far (not used it much though).