VATS is going to be the one thing that I can't figure out yet for this. It's one thing to stop or slow down time for a single-player game for VATS, but in multiplayer? That's going to be messy. Either you need to constantly slow your game down, or come up with a whole new system for VATS, or remove it entirely.
I had been thinking of that too...
Fast-action combat can be uninterrupted while having VATS specify where you want to place shots and just simply place your crosshairs over a hit-box or center-mass to let the computer handle the rest a-la auto-attack.
Else, turn VATS off and run with free-aim.
The only way I could see it not negatively affecting 6 teams of 4+ players where everyone has access to stop, or, even slow play..
Would be to have a hot-key location-targeting mechanic.
Either through specific hot-key buttoning for fast select or KeyPress+MouseWheel to scroll through hit-locations, or ... Whatever mechanic is used in those god-forsaken game systems with controllers that have more than two buttons....
I think MWO Targeting Computers could have benefitted from something like this (unless they already do, because I stopped on account of creative differences over Clan implementation, I don't know how they function there).