Well, Pokemon Zeta has this doesn't it?
They have 1-4th gen pokemon following the trainer, but not Gen V and VI.
And like you pointed out, that's the thing: There's no sprite for Gen V and VI pokes. I don't believe Ame would want to add only Gen1-4th pokes. If sprites for Gen V and VI existed, then maybe.
The idea is nice, probably has been suggested before, but i doubt it's going to happen. I'm pretty sure it's not going to...
But hey, what do i know?