Neither brings much in the way of IP to the table, except maybe Shantae, which...fine, whatever. Mercury Steam seems like the more flexible dev, able to do more, and if their Metroid game is a hit, then they could become a solid prospect.
I'm in the camp that Nintendo needs to staff up immediately because they're going to have to self-support the Switch for the next couple of years; but even so, I'm not sure either of these studios is the way to go just yet. A big pickup with lots of IP, several studios, and PC development experience would be much more to Nintendo's benefit (which is why I think they should start seriously looking at Sega--their legacy content alone would be a big boon for any future Virtual Console-like).
TL;DR: Neither for now, but put a gun to my head and I'd say Mercury Steam is the better pickup.
EDIT: On second thought, Wayforward's 2D experience might make them the right vehicle for Metroid, moving forward. On the other hand, Shantae always felt artistically accomplished but kind of, I dunno, lifeless.