I agree that all-powerful Summoners, or an all-powerful League, makes storytelling hard. To me, the obvious solution is simply to make them not all-powerful. Specifically, the way we've handled it in Factions, the League's legitimacy is not based on it wielding such OP magic that it could singlehandedly obliterate anyone who dared oppose it. Rather, its legitimacy is founded upon the fairly even balance of power in Runeterra, and the support of crucial factions such as Demacia and Noxus. In the Factions universe, the League is walking a dangerous tightrope, trying to carry out its mission of preventing another Rune War (which often means giving orders to Demacia, Noxus, and other factions) while being mindful of the fact that, if these factions ever chose to simply walk away, they'd crumble.
The main old-canon example is Kalamanda. I personally don't see that as being about the League's omnipotence. Instead, I see it as the League making a dangerous play and surviving the consequences. Sure, they can lock down Kalamanda and forcibly stop the fighting there, but (at least in my view) this only worked because Demacia and Noxus agreed to call it quits. If they'd decided otherwise, the League would have collapsed.
It's sort of a "Marshall has made his ruling; now let him enforce it" problem. I think that's a really interesting tension, from both sides of the table: the League trying to carry out its mission of reining in the factions without going too far, and the various factions constantly asking whether it would really start another Rune War if they just this once told those annoying League Summoners to get lost.
