The gameplay may be essentially the same, but the game as a whole? Not necessarily.
The point is, by adding a preexisting brand to a game, you're inherently limiting what it can be. With the Mario brand, the game has to "fit" into the Mario mold.
By trying something new (original characters, setting, all that jazz), though, the sky's the limit. There's freedom to create something radically new or fresh, something people haven't seen before. Maybe people will respond it, maybe they won't, but you'll never know if you don't try.
Plus, adding an established IP isn't always good for a game either. When there's so many Mario games being made (Wasn't 18 the last count?), it can be easy for one to get lost in the shuffle. With its own identity, a game can stand out and shine.