...uhh, something I should point out?
Apparently, the Majora's Mask bosses
are sitting at ~500 gigatons via Gyorg, and since Gyorg is fought later on beyond Odolwa in a game where there's a clear natural progression of strength that seems to mean Odolwa is somewhat below that to an unknown extent. Really, only Twinmold is "possibly" Large Island level+. ...my bad.
That said, even early on Link is a good deal more skilled than any Omastar, I'd think, and Odolwa seems to be able to keep up with that, so I'd say Odolwa is the more skilled combatant...
Though, Omastar is probably far more maneuverable (ironically), given its far higher general (non-combat/reaction) speed, and has more AP/Dura and a slightly better movepool... which should be enough to take the win, high-difficulty-
One important thing, though. The whole premise of the first fourth of Majora's Mask was that Odolwa being in the Deku marsh had corrupted the whole place's waters with its miasma of death or whatever, and it resulted in it being wholly unlivable for aquatic life.
...Standard Battle Assumptions in place, wouldn't both combatants start out where they're strongest? I.e. in a body of water, since Omastar is a Water pokemon based directly on an aquatic lifeform and Odolwa doesn't care either way? If so, I imagine that miasma would re-generate itself in all of the water surrounding Omastar, and it probably isn't intelligent enough to figure out what exactly is happening to its environment before it keels over and dies by virtue of Odolwa standing there and not getting gibbed within a few seconds.
Inconclusive, I guess, since it really depends a lot on the specifics of how they run into one another.