I very much like the consequences of overheating (which might necessitate flamers and the like being rather weak), and Ammo explosions. However, ammo explosions should not happen because of a random dice roll for a critical hit. It should be based on well placed shots in spots that are already weakened for armor, or done with weapons that are fairly good at armor piercing. Missiles, for instance, should be more or less awful at that.
I'm also an advocate of extensive customization taking a large amount of player skillpoints and money to do, starting off with more or less Stock only, moving on to other TRO designs, then letting you swap out a few similar weapons, replace large ones with multiple small ones or vice versa, and finally move on to where you can get more or less a full customization experience... within the reasonable design constraints of the mech. Swapping a large lazer for a PPC, I think, should be more of a mid-range thing. Swapping a large Lazer for an SRM rack? More endgame. Changing to an XL engine or something like that? Pretty much maxed out in the customization category.
Speaking of which, Omni's probably shouldn't even be pilotable until you hit the mid-range.