It's not just the aiming, it's that there is really no point in using portals in Mario. You need them on Portal because there is no way to advance without them, obviously, but on Mario, simply jumping on the enemies is enough, so the portals end up becoming a hindrance and using them consumes more time than if you just played it normally. As it is, it's nothing more than a novelty. The premise is interesting, but portals were obviously not made with Mario in mind.
I can't think of a game that could benefit from having portals in it, actually. Maybe Worms? Sim City 4?