So let’s look at the 2012 Tour de France route (only GC climbing opportunities) once again:
1. Belles Filles (stage 7). This stage can be subjected to your first point, not quite mountainous stage ie the questions may stand after it, but I would let myself be that impudent to compare that stage (or rather what theoretically may happen to GC there) to Verbier 2009

Both stages are about 200km with the only place to attack on the final ascent, there was no hard racing in several days before Verbier and so will be before Belles Filles. Verbier is 8.8 km - 7.5 %; Belles Filles is 5.9 km – 8.5%. Of course Verbier is 2.9km longer which does matter in the case of that you should reduce the bunch first before attack, but the profile of Belles Filles offers the steepness from the bottom of the climb so I guess it’s possible for the best climber to go solo for 3-4km to gain at least 30-45sec going all out.
2. Alps. 1 GC stage. I agree that the Colombier stage is pretty unfortunately designed and the most likely won’t cause any gaps between the main contenders but I don’t think it means there won’t be any attacks there and the peloton will ride it that easy to say they approach the next day’s La Toussuire challenge fresh. Don’t get me wrong, I don’t argue that it’s bad that the Colombier stage isn’t as hard as it could be with better designing but imo you can’t say it is wasted in terms of possible hard riding in context of next day. So the next day, La Toussuire. Despite only 140km length thrilling altitude gain and uphill finish for the very best.
3. Pyrenees. 2 stages. The Foix stage is just wasted and I really don’t know what’s the point of making a flat stage to Pau (apart from money) before 2 decisive Pyrenean stages to Luchon and Peyragudes. Both these stages are hard and can change the GC.
So in fact we have 3 GC mountainous stages and one medium mountains GC stage with mtf.