Are you having any similar issues? What is your environment like?
One thing is to have the DBs and FillDB on fast storage, preferably high iops and low latency. Not spinning disks. If the DB and Root are on separate systems, having a 10gig link between them is helpful, and same goes for the terminal server where windows console sessions are taking place. Having the console caches on fast storage is also a good idea, and redundancy doesn’t matter quite as much.
IBM has made some tweaks to help on the platform, as well as adjusting some settings. Increasing the console refresh interval for all users using BES Admin tool helps a little, but if you do that too much you really start to loose the speed of results which is annoying.
It might make sense doing it all over again to have custom sites that were a little higher level instead of having custom sites for every little sub group when they might not actually end up being used. If there is a real need for it, then sure, make it, but otherwise I think having less is better.
Another thing I’ve done lately is have some sites and custom sites have a delay of when they will be subscribed by the client to speed up initial provisioning and installation of software with bigfix for new machines. See here: Delay BigFix site subscription to speed up client provisioning
It really depends on what issues you are having as far as what areas to look to address those issues.