I think Kin is more or less right on the money here. I've been drilling my boxing intensely for the last few months, and one of the things that I've realized is how big a difference rotating the hands makes in enforcing the power and speed of the punch, because it forces turning over the shoulder and the hips. If that turnover is managed in a time-efficient way, then the punch is really very effective.
I don't feel like punching that way is as powerful. I think curious1 hit the nail on the head, in that, vertical fist is more pushy and lacks snap. That said, I like to throw vertical-fisted uppercuts sometimes, since the twisting of the fist (or lack there of) doesn't affect the mechanics of the punch at all. It definitely does slip through people's guards better.
As far as penetrating the guard, I've never been partial to banging in against my opponent's hands while they're keeping the guard up, and in MMA it seems like a massive waste of energy. If you're comfortable with it and get good penetration on the punches, then that's great. If it works for you, go with it.
My preference is to force the change in position of the guard, or to attack around it. One of the things that I've been working on with my hands is attacking different regions of the face, particularly the ears and temples through the typical guard. Even with the big boxing gloves, I've found that if I don't try to penetrate the guard looking for the button, but focus instead on areas that aren't immediately protected, I can create the kind of holes that I want to get those shots in on the nose or the orbitals. [And for those who are more focussed on striking the face, rather than going to the body, this is a good alternative, since it doesn't require a change to the body blow stuff.]