1) No native IMAP support 2) No native Exchange support without a BES 3) Horrific attachment viewer. 4) No real-time spellcheck 5) No auto-correction 6) No easy way to sync contacts/calendars over the air 7) No (minimal?) HTML e-mail support (unfortunately sometimes it does help make long e-mail chains more readable) 8) Gotta rely on your carrier for push e-mail -- or in the case of Sprint "Oh yeah we'll send it if we get a chance. Give us like 20 minutes K?" e-mail service. 9) No intuitive way of deleting lots of e-mail messages that don't happen to all be sequential to each other in the list. 10) No folders -- just one big flat mailbox. Hard to save messages on your phone this way. Again, fixed if you have a BES but I don't want my $200 SmartPhone to require $2k-$5k in hardware/software to be functional.
It certainly gets the job done for the basics but once you get used to having more options and flexibility it's hard to go back.