I think you just answered your own question. Regardless of other Pokemon in Ash possession Goodra is a powerful Pokemon. And the issue with having really strong Pokemon is that everything becomes to easy. If everything is easy, the show becomes boring and stale, as Ash can just blast Team Rocket away with a single hit. The most prominent example of this is Charizard, who's extreme power made it unfair to any and all who came across it. A show needs some variety, and struggle, to remain interesting (I haven't watched the show since early DPP, so I can't really tell if it's great or stagnant or bad). But I am absolutely sure that if Ash is in possession of such a powerful Pokemon he might leave it in some manner, not because it makes sense from his perspective, but because the show must go on and stagnation kill all media.
