Issues I had with HTC Android that are solved for me now:

• com.android.phone process no longer crashes every now and then. When it crashes you have to enter your pin-code to be able to receive phone calls again.
• I don’t use HTC Sync so having the pc synchronization process always running was wasted memory.
• I don’t use the facebook integration in contacts since I’ve already synced contact photos with my gmail account and I think the facebook app works better for looking at the facebook news feed. Since the facebook/flickr/twitter sync process is always running in HTC Android regardless if you use it or not it was wasted memory and cpu usage for me.
• The HTC Calendar does not have a week view, the Android calendar does.
• The HTC Browser is always in full screen hiding the notification bar, I prefer the original Android browser that does not run in full screen so the notification bar is visible.
• The Android browser seem to crash less than the HTC browser.
• com.htc.android.htcime leaks assets and asset managers everytime a keyboard is shown.
• The phone seem a lot faster running vanilla Android compared to HTC Android.
• com.htc.android.mail is always running even if it is not used, wastes memory and cpu.
• 3G connectivity seem a lot better now, with HTC Android the phone would drop the 3G connection and never reestablish it until I manually did so.
• Integration between the different apps is much better in vanilla Android. For example, in the messages app you can see if a contact is online on gtalk and a lot more neat little contact shortcuts.
• I prefer the look and feel of vanilla Android compared to SenseUI.
• And there are a lot of nice new features in Android 2.1 compared to Android 1.5.

For how I use my phone there are a few issues with the Android 2.1 ROM on my HTC Hero:

• Camera does not work very well.
• Battery drains a bit faster, it lasts a day (~13-16h) for me now.
• Gallery app UI is corrupted when changing orientation.

And of course since vanilla Android does not contain SenseUI there are no HTC widgets, HTC keyboard or HTC quick dialer. But so far I haven’t missed them.