There's really no good reason for any original character to not return, and Falco definitely ranks high in originality. In the StarFox series, Fox and Falco are strikingly different characters with great contrast in their personalities. While Fox is consistently the love-sick authoritarian leader, Falco plays the part as the obstanant smack-talking rebel, constantly leading to disputes between the two. What's more, in reference to actual gameplay, despite having the label of "clones," they're both played with radically different styles and are mostly incomparable. Falco offers a contrasting persona and a totally different playstyle from Fox, so his originality should be enough to score him a spot on Brawl's roster.
Now, assuming Falco makes a return, we're then faced with the whole "de-cloning" issue. There's really no need to make drastic changes in Falco's abilities due his afforementioned differences in playstyle. If Sakurai is so exceptionally devoted to ensuring that no two characters share a neutral air, then trying to put any decent quantity of characters in the game will create a mess of senseless movesets. The only thing that should dictate the label of "clone" is how the character actually functions, and seeing as Falco functions entirely differently from his counter-part, there isn't any reasonable need to alter him too greatly. Unfortunately, this lies entirely at the mercy of Sakurai's desires.
...doesn't really matter though. I just want Ganondorf.