Adding more Commandos sound pesky, but lowering the Arach count a little and raising the Commando count a little more might do the trick. On the other hand, I seem to have no cell problems at all. Usually I find myself dropping hundreds, keeping around only 100 for the BFGs 3 more shots. PRs waste ammo too quickly to keep them around - even with plenty of ammo pickups, getting caught with only a PR means running the risk of running out of CURRENT ammo - and me no like that. CGs waste ammo fast enough.
As for RLs, someone said somewhere that since using a RL can be so inconvenient at times, masses of rockets rarely mean too many. You keep 20-30 around, and when it's finally a good time to use them (no loot to ruin and not too close) you end up using most. Then you refill the stocks, 'till the next case appeares, not often in the near future (unless it's AVs, in which case there can't be too many rockets).
And as for shotguns, effectively they have 25 shots per stack. That's only RL*2.5, and you use it way more often, so of course you run out :P Maybe keep a CmbtSG around (and I have another idea, I'll be posting in a moment).