Mail app does not recognize .ics files as calendar invites, lack of this simple feature makes calendaring with the rest of the world impossible.
There is no OpenVPN or VPNC client that works out of the box. I had to hack it to get it to work.
Battery life is terrible, lasts at most 2-3 hrs.
Mail for Exchange does not work as advertised. Can’t get it to work at all. Very vague errors messages.
There is no ability to search email.
No ability to search across all apps; even PalmOS has this back in 1994.
You cannot delete an email without opening it.
The standard Jabber client will not connect, but the hacked-up Pidgin client will.
Too many competing mechanisms/apps/conduits to sync email/contacts/calendar.
Cannot import .ics files or .vcard files, so you are stuck using some other conduit or 3rd party, if you can find something that works.
Does not support any “standard” sync protocols except Exchange, which doesn’t work.
I could go on and on.