Well Other M was definitely closer to a 2D game than the Prime games were, and if NSMB wouldn't have happened before, I don't think Nintendo would have dared to put 2D sections in their big games like Other M or Mario Galaxy 2.
I think that IF we happen to see a new Metroid during the upcoming console generation (3DS and WiiU), it will be a sidescrolling game. Chances are high that the franchise will skip another generation and then be reinvented completely again though.