I think enemies should do 100% damage to the PC in VATS, instead of the 10% like it is now; with current VATS, one can simply wait for a charging enemy to get into point blank range, and cue up shots with a powerful weapon for an easy kill as enemies' damage is negligible - even with powerful ones like Yao Guai or Deathclaws.
Of course, this makes it possible for the PC to die upon exiting VATS (which I think is the reason why Bethesda included the 10% damage rule), but is this really a problem? At least it would make the use of VATS a bit more strategical.
Also, I'd like to see Action Points spent on entering the Pip-Boy during combat - this prevents healing/buffing during combat and should make combat a tad more challenging.