I don't think it would be a system seller, it would be a franchise killer.
I really doubt Atlus could just keep doing their stuff as they like on Nintendo, not to mention eventually it would end up like other smaller games published by Nintendo that have never come to the west or the ones fans had to beg for it and someone else brought them over.
Don't get me wrong, I love a bunch of Atlus games on Nintendo's platforms (especially the portable ones) but I think them being owned by Nintendo would be a big hit in their creative freedom.
I also don't want Sony to buy them, as I'd prefer them to stay 3rd party, but at least Sony seems to give its developers much more freedom to try new stuff and time. The time it took for GT5, the game from Team ICO that never got released, their Siren team that also took their sweet time to make Gravity Rush and so on. Now the first two were huge money grabbers but Atlus games are a lot cheaper to make and have much smaller goals, so a game that takes forever to be made like Persona 5 could take its time and be ready just when it's ready.