I honestly doubt that Bowser will be nerfed, I do recall Sakurai mentioning that Wiifit trainer was strong against characters like Bowser, and she's very likely not the only one. Bowser did well in the 3ds even for a few reasons. First, the format of the tournament was highly favorable to Bowser's moveset, FFA items on with time-based matches where K.O - Falls were the win condition. Experienced players would recognize this and use Bowser since he'd already been shown to be strong in FFA games at E3. Second, there were the players using him, the two guys at grand finals probably could have gotten there with any characters, but they picked Bowser because he simply worked the best in the format. Finally, why they stuck with him in 1v1, is because no one knew how to fight him properly. Toon link wasn't abusing projectiles and certain aerials like bair, and Shiek wasn't abusing mobility, Ftilt, aerials, and bouncing fish. Bowser was never a very popular character in any of the versions he's been in. So it would not surprise me if most of the players had never even played a serious Bowser before.
I was at a Brawl tournament recently and actually met some players who were surprised that Bowser could koopahop. Koopahopping is one of Bowser's most well known tools in Brawl so that just shows how obscure he is as a character. Then Bowser gets a major overhaul and even the players who knew how to fight him have to make adjustments. So I really wouldn't be worried about the big guy getting nerfed. I'm pretty sure his current build could make it into the meta since he still has the same weaknesses as before, it's just that now they are easier to hide. Also, I do remember Sakurai mentioning that he didn't like the idea of simply nerfing a character just because they have some good tools; seems like Bowser will be fine.