Honestly yea, I feel like I had this problem in Mech Commander 2.
Fielding 8+ Anibus rocking double clan long-range missiles and a medium range PPE was better than pretty much anything else, plus those little guys came with radar, always turned out easier, and faster than throwing 2 or even 3 Assault class mechs into the map. Death by a thousand cuts. Plus, it was easier to split focus, because you just had so many more options. Send 3 Anubis here and 4 there? Ok! Or split up your two Atlas? No, cuz they'll get flanked in a heartbeat.
Be the swarmer, not the swarmed.
So maybe we should accept that the rules are balanced too well to mess with the way we want to all the time.
Additionally this may be of use; viewtopic.php?f=33&t=597
Maybe all 'weight class rule mods' could be its own section? There seem to be a number of them...