Exact same issue here. I have a Mac Pro 2.8 (mid 2008) with 20GB RAM, and since the Lion upgrade, it wakes up very slowly (approx 40 to 60 seconds), and sometimes drops back off to sleep before the login screen appears.
The fans go full power for much longer than they used to do in Snow Leopard, which gave a quick blast then woke up pretty silently after that.
I am genrally getting various issues, and have posted another thread re. not being able to calibrate dual monitors with Lion, and Screenflow not recording from the scondary monitor.
There are many bugs in this first release of Lion. I wish I had held back. I never expereinced anything like this when I went from Leopard to Snow Leopard.
Serious considering reverting back to SL, but not certain I will not loose things along the way.