Why would Retro need to collaborate with SK on ED2? They are 2 separate developers capable of working on 2 separate games (with supervision from Kensuke Tennabe of SPD 3, of course.) I doubt Nintendo is going to tie up 2 developers, including one of their most talented, working on what will be a niche game.
SK is a lot smaller than it used to be. I don't think it makes a lot of sense to partner them up with Retro, but they are going to need assistance on whatever their next big title will be.