amigahardware has an proper explanation afaik.
anyway only downside i know of is that you cant:
1. use a ppc card with it
2. you cant use os3.5 nor os3.9 with it (there is a patch but it costs alot of money and hard to find)
3. and there is no aga
some of the cool stuff:
great Mem speeds
improved a4000 styled design (faster and less buggy)
about the tower...check amiga hardware site.