There are a number of studies comparing the effectiveness of various center-fire rounds. There is also an FBI study that evaluated a lot of shootings. The answer most of these studies point to is that SHOT PLACEMENT is far more critical than caliber -- assuming that the round used has the power to penetrate far enough to do damage...
I'm oversimplifying in the following comments, but this type of discussion often requires simplfication...
If you can place a larger round in the bad guy's central nervous system, you should use a larger round; if you can't shoot a larger round well, you'd be better served trying to get CNS hits with a smaller round than missing it with a larger one. (I don't shoot .45s as well as I shoot 9mms -- so I'll continue to carry a 9mm handgun when I can. Some folks I know shoot .45s better than I shoot 9mms, and they'll continue to shoot .45s. I think those are wise decisions, in both cases.)
The capacity question seems important, but it may be more of an an intellectual issue than a practical one, for unless you're missing with a lot of your shots (which might happen in high-stress situations), all those extra rounds (12 vs. 7, or more realistically, 17 vs. 8 or 10) won't matter that much, because in most self-defense encounters things are generally over pretty quickly, with relatively few rounds fired.