There really isn't much of anything RIM can do short of not using MAPI ... which we'll hopefully see soon enough.

That said, I heard from WES last year that RIM uses 15 Messaging Agents per BES with a max of 100 users per agent. Now that info is over a year old and BES 5.0 has been deployed, so I'm not sure if it is different ... but that is how I heard it was with 4.x.

But honestly, as a first step you could at least minimize the number of Exchange servers each BES is communicating with ... move what users you can; it very well may fix the problems.