Hard to say, mainly because there are few official teams for the player characters. However, I can certainly say that Red would not be, despite the fact that a lot of Pokemon fans consider him the ultimate trainer. If one plays the entirety of Gold and Silver and the remakes, they are meant to beat Red to show their skill. Maybe it's unfair to the character, but as far as we know, he's the only one that can truly be beaten in the games.
The gen 5 protagonists(Black and White in particular) are a good choice, primarily since they are forced to capture at least one Legendary Pokemon which ups their power level. The same could be said for the gen 6 protagonists, and they can use mega evolution as well. Not to mention, ORAS forces you to capture a Rayquaza who can mega evolve, and we all know how grossly overpowered that thing is.
I think the only way to determine this would be to look at the Pokemon Adventures protagonists. I think that would be a more accurate way to look at their personal strengths. My favorite would be Black from the Black and White chapter, if primarily because he owns a Reshiram, and I like his design. I cosplayed as him at Anime expo after all! XD I can't say he would be the strongest since I haven't read much of the manga yet.