Well I'm all for Vaati simply because I think he'd make for a more interesting Brawl character to play, but to be fair, the idea that that the developers only have a choice between putting only in the most recent form of a character or not putting that character in at all is just silly.
Your argument seems to be based on the evidence that all the Brawl characters that have already been announced appear in forms that are similar or exactly like how they appear in the latest games featuring them. That seems to be a pretty flimsy support for your argument given that we have yet to see the vast majority of the characters that will inevitably be in the game (i.e. there is a very high probability of this being purely circumstantial).
Supporting the other side of that argument, however, is the idea that the people making the decisions about these kinds of things want the game to be as successful as possible. I think this is a reasonable assumption.
If it were determined that more people would buy and enjoy the game if they included an older version of a certain character rather than the most recent one then, assuming no outside force (legal, economic, or otherwise) was stopping them, they would do it. I think it is likely that the developers would arrive at such a determination when considering MM Skull Kid vs. TP Skull Kid, so unless Sakurai went completely wacko and said
"You know what, let's forget about making a successful game! It's more important to avoid including any versions of characters older than their most recent ones!", the only thing that would cause them to include TP Skull Kid over MM Skull Kid would be an outside force (pressure from Nintendo, perhaps as a misguided attempt to promote TP, but even that seems very unlikely).
Of course, all of this is hopefully moot, because Vaati would make a much better Brawl character anyway!