Well, in the Batman/Superman story where the two versions of Bats and Supes meet each other (early in the careers of the Prime versions, apparently just before the invasion of Earth-2) it was said the younger versions were darker, more violent, aggressive, something like that.
And that weird being who caused two other universes to merge with the pre-Flashpoint universe during the Sept. 2011 reboot did say it was done so that there'd be a universe strong enough to deal with the 'big badness' that was coming.
And so, as you said, "Prime-Earth does appear the more potent universe."
The only problem with that is, that the big bads were already soundly defeated pre-reboot: Darkseid, the CSA, the Anti-Monitor, Neron, Nekron...
Till now, all we have seen so far are rebooted old menaces. And coming nex: "The Anti-Monitor!", who seems to be the big badness again, which doesn't really make sense so far, with Pandoras explanation, since he had gotten his butt kicked already.