Regardless of whether the criticals system in VATS has been done in a way that works well in an RPG (I'll withhold judgement until I know more), I really don't think the argument that "Once it's core mechanics, not using it, is not playing the game" works. There are many core mechanics that you don't have to use. Stealth is a core mechanic, but many players will choose never to use it. Will they not be playing the game? Heavy weapons are a core mechanic. If a player sticks to stealth and light weapons, will they not be playing the game?
The real question is, is the crit-meter in VATS a core mechanic with no alternative mechanic to take its place, and which is essential to surviving fights? VATS itself is a core mechanic, but while it gives an advantage in fights in FO3, it is not essential. And there are now alternatives - players can just choose to use the action points that power VATS for sprinting, or using jump-packs, or whatever else action points are now tied to outside VATS. In older games, as far as I'm aware, there weren't even alternatives to the VATS core mechanic, but because it became non-essential in FO3 it was valid to not use it. You traded the advantage in combat for excitement and fluidity, basically.
Even if there is no alternative to using the crit-meter, it seems only to be a component of the no-longer-entirely-core mechanic of VATS.
For better or worse, it seems to me that in FO3 Bethesda downgraded VATS to an optional core mechanic, but didn't put in any optional alternative. They've now put in optional alternatives, and added a feature to the optional VATS mechanic.
Seems reasonable to me. I may not like it, it may be implemented very badly, but I don't think it's an intrinsically stupid change.