Not so much the Chao Garden, but the Chao in general seem fairly neglected these days. Aside from one extremely difficult to find cameo in Unleashed, they've mostly been filler for crowd space in most games so far (none of them even mainstream games either). I wouldn't mind the Chao Garden returning if it were tweaked to be, oh I dunno, less boring and more involving, but really now, it would just be nice to see Chao back in some significant form at all.
Actually to be honest, I've always been hoping for Sega/ST to make a self-parody game of some sort, using Chao versions of the main characters to that effect. Doubt they're ever do one or the other, but that would be pretty fuckin' sweet.