A platformer can be in 3D. SM64 is in 3D, but its platformer half has the same amount of charm that its adventure side has. As for SMS, I kind of agree it had a somewhat complex plot. However, because the full plot wasn't entirely in depth, I don't find it to be very complicated.
As for SMG, they should put Luigi in it too.
Oh, and when I look at complex plot in a Mario game, I consider how big a reason the main bad guy has for kidnapping Peach, and how complex his/her scheme is. If Peach is like a key for obtaining some world-conquering thing, and not simply because the bad guy has the hots for her, that's gonna invlove a nice, complicated plot. Villains like the X-Nauts and the Shroobs have a goal similar to one of Bowser's, only on a much larger scale. Instead of just the kingdom, these guys want to conquer the entire planet.