Maybe this is true, maybe it isn't. However, in this post-AVENGERS world we live in, I have a feeling we're going to be seeing many more crossovers. One beloved brand isn't enough for one product anymore, we gotta cram in as many as possible! No company is more ripe for this than Nintendo. It's actually surprising they didn't start doing this all the damn time after the success of Smash Bros.
This specific idea, however, is really unappealing to me. Metroid is my favorite franchise while I'm thoroughly indifferent to Star Fox. Having Star Fox levels break up a Metroid game sounds terrible. If this is just a misunderstanding of the truth and this is a straight up Metroid game with Star Fox-esque levels, that sounds equally as terrible. It would also suggest that Retro would be continuing with the segmented areas/planets that Metroid Prime 3 used as opposed to the giant, contiguous worlds that Prime 1 and 2 and every other Metroid game used. Like everyone else who has ever lived, I greatly prefer the latter.
Going back to the mash up idea, maybe you can play each mode separate from the other? Then why bother? It would just make more sense to separate the games and charge $60 for each of them. There are ways to do these sorts of mash ups well, but on paper, this doesn't sound like one of them.