Let's look at what characters are revealed as ATs: Hammer Bros. - generic Mario minion, no one expected him to even be in the game, Nintendog - odd character from it's own DS game, again no one expected it to be in the game or playable (other than from the E3 trailer), and Goroh - a character a lot of people *hoped* to be in Brawl, mostly because they wanted a Captain Falcon rival and more F-Zero rep.
Well, we are not sure about additional rep for F-Zero yet; it is too soon to tell. Looking back, Goroh wasn't even on any of the Sakurai character polls. The only other F-Zero character to make it was Black Shadow, who could easily take the villain roll for FZ if they so chose to put him in.
Really, there is no reason to worry about any character at this stage. So far, it seems to be, that ATs have been added to keep characters around who wouldn't otherwise be in the game, not to downgrade those characters who all expected to be in. So...yes, some retro characters are at risk, but this was expected anyway. No one truly expects 10 retro characters to be in the game. The gift, now, is that more will be in than would have otherwise been. As for Ct. Olimar...I really don't see why he was even brought up. So he is a little obscure? So what? That is what smash is all about...bringing characters of all kinds together. Nintendo is going to want to show off it's new series; I have no doubts Pikmin will have rep as a *playable* character. For crying out loud, he is one of the top 7 or 8 choices based on the character polls with 3 mentions.
So, I'd wait to see some better evidence of this before I got my panties in a bunch...