Since Metroid is a premier IP, it needs premier treatment. Therefore an eShop release shouldn't even be up for debate.
Since when is Metroid a premier IP? It doesn't even have a dedicated studio. Sure, a lot of Nintendo fans act like the series is a big deal, but compared to other Nintendo series, Metroid is small-time, selling on average under a million units a year throughout its history. Your beloved NSMB2 will probably outsell the entire Metroid franchise singlehandedly.
Besides, WayForward tends to take on a bunch of projects at a time. I think they'll have a total of five games released in 2012. They probably don't have or aren't willing to devote the resources to make a retail Metroid game.
Though now that I'm thinking about it, I suppose Sakamoto and at least a few other Nintendo employees would be devoted to any Metroid project. So if Nintendo wanted to do a collaborative effort like Other M, they could. I'm just worried about how well that went the last time.
Love and tolerate.