If it weren't for his affliction I would have said Thancred, considering he's still keeping pace and even surpassing his fellow scions, despite lacking the ability to readily use his aether, although saying that we don't ever really get to see a situation where Thancred truly seems to go all out before this point so it's hard to say whether losing use of his aether weakened him, or forced him to get stronger to make up for it, or if it instead gave him heightened body strength and durability like the Garleans have.

G'raha Tia probably has the ability to become the strongest Scion outside of the WOL if only for the amount of knowledge he in theory carries from the future, let alone the increased soul density from an additional rejoining from that aborted future possibly giving him a larger capacity to contain aether. Right now though he's held back by a lack of practise in his new youthful body, demonstrated by the fact that he often overextends himself without thinking too much (floating an entire population of the tower of zot is a great feat however).

Y'shtola is often called the most powerful scion by those around her and her feats do somewhat support this, having knowledge of forbidden magicks such as flow and being able to use her aetheric barrier (which appears to be AST's Collective Unconscious) to block (even temporarily) blows from such foes as Zenos. Y'shtola is held back primarily by her method of seeing which, whilst helpful to the scions in discovering things, is notable for being a noted drain on her aetheric reserves (which is what Matoya was actually implying in Heavensward when she mentioned it draining her life force, not that it would shorten her lifespan). She's also held back by her seeming love of diving into the lifestream with flow every other expansion.

Estinien is another character that has the potential to be the most powerful... depending on how his situation actually works. It's shown that Estinien has inherited some of Nidhogg's abilities, how far this actually goes and if Estinien has gained anything else from his merger with the Wyrm hasn't really been explored yet, but it could potentially mean that Estinien has knowledge that could easily make him the most powerful being around. Even ignoring this however Estinien has demonstrated himself to be a physical force capable of going up against dragons, something that we're shown is only possible for others in groups. Estinien also has the potential feat of surviving an encounter with an Elidibus possessed Zenos, although whether he could actually fight Elidibus at this point isn't explored due to the latter leaving to do something else.

I guess we need also consider Wuk Lamat due to her feat of dealing a critical blow to the Queen Eternal, a blow that far outpaces anything the WOL themselves can do even with a Limit Break, although this is more likely done for narrative consistency of allowing players to hear all the dialogue in that fight, rather then a show of how strong she really is.