outright told he made the multiple universes, that he attacked 'em head on before, but this kinda goes with the whole arc in general. all 3 universes of legion are creations of Prime, all to take out Supes. but really, by the way he says it there, probably are more that just... kinda died off. >_>;
"some kind of virus", 'cept prime doesn't kill by a virus. time trapper however does know how to make blood like oil and eat your organs away. ergo, yes, he's used that power as well.
effectively the main issue comes down to you just can't wipe supes out. you can't wipe his influence out, it's impossible set by the ultimate being in the multiverse in the first place (or rather, set by the incarnation of dc comics itself). so yes. he's going to do anything he can to mess with supes there. like say, time travel a pair of people he killed with his powers as time trapper, each from a different universe, then bring them to the past to dick with supes.
so no, he most definitely uses other powers as well. just not against supes since supes is who he wants to destroy entirely. just not himself because that would be incredibly dumb (which his younger version has no problem being) and can cause a time paradox.
now personally i actually can totally see prime beat darsh down there. each dispel bound shield only has one property to it, he's got multiple ways to attack, and it's not like he'd simply stop attacking. the limit of each one is that it takes attacks up to a nuke level blast and takes the leftovers. fine, but nothin' really stopping prime from just dealing continuous attacks. each one takes the 'full' one but there wouldn't really be an end to 'em. time powers, mass alteration, tk, portals, heat beam eyes, whatever he did to those people's bodies, and punching the hell out of it would all be plenty strong. pretty much anything he does would be nuke level in the first place and he'd just continuously plow through 'em. it took the full attack, fine, the next one's right there anyway. the only thing you'd actually do is end up irritating him and pissing him off which tends to get him even crazier. which prob happens anyway since darsh'd likely end up supercharging him.
likewise on that end, bloodstone really isn't the end all spell to use either. one thing all supermen have in common, prime especially, is that they can take their own attacks easily enough. prime doesn't punch hard enough to destroy the universe, but he sure as hell can (and did) tank a blast of that level point blank as superboy (meaning, weaker). of course nobody's actually seen how the spell works but considering prime's got workarounds to it anyway with portals and the like, not that big a deal.
in terms of regen... prime doesn't have it in the traditional sense, but you do see him heal extremely quickly. he doesn't regenerate organs and the like, but you certainly see him and other kryptonians at times look like nothing happened to them at all in extremely short periods of time. prime being the biggest oone to this, especially in sinestro corps when he went from beating down people, getting in trouble due to his at the moment issues of too much red sunlight exposure (doesn't exist here or by the time legion went down) and got beat down, then the sun came out and poof, healed. healed enough to beat down the best green lantern possible that was a superman-clone with the full power of the corps, followed by flying through a universe eating being made of anti-matter to chucking said being to the end of the universe and not looking like anything happened to him
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The future must protect the clone's past.
"Maybe it's a tentacle, molesting the planet itself. - Aschen Brodel.