As far as I know you get no payment at all from Nintendo until you hit a certain number of downloads (within a time-limit). Digital downloads are up lately, but I think it's still a very lofty target for that platform. The eshop is still a pretty poor user experience. That coupled with the dev kit cost... I really wouldn't invest in it unless I had an iron-tight sure winner or two ready to publish.
IMO Steam is a ridiculously better investment of time/effort/money. I would definitely get that done first, then maybe port to Nintendo if it did very well (even then, knowing it's probably largely an expensive advert for the steam version to pick up sales again, and let's be honest - a bit of a vanity thing).
Nintendo might have changed their rules a bit lately, or at least by the time you're up and running on steam, so my advice is to revisit this question then! Certainly wouldn't make any design decisions based around a possible future console version though, just make the best product you can for Steam.