So how do you provide some sort of shakeup to the Mario universe? Well, the easiest would be to provide a different villain of course. Most of the spin-off games have done so whether it be Smithy from Super Mario RPG: Legend of the Seven Stars, Tatanga from Super Mario Land, or even the lame Princess Shroob from Mario & Luigi: Partners in Time. Is it impossible for Bowser to be knocked from the antagonist to no role at all in a main Mario game?
I think there are several characters that Nintendo can use that would allow for them to keep a familiar formula, but shock players when they reveal the new villain at the end. Here are some characters I wouldn't mind seeing replace Bowser:
Donkey Kong
Perhaps everyone forgot a particular game from the arcades featuring a monkey who kidnapped a woman and decided to wreak havoc on a known plumber using barrels? Well, that wasn't Donkey Kong. No, that honor would go to his father/grandfather (games conflicted with what his relationship was exactly) Cranky Kong. And while the original Donkey Kong arcade game wouldn't provide a good enough motivator for Donkey Kong to seek his revenge on Mario, the followup game does. In Donkey Kong Jr., Mario kidnaps Cranky and locks him in a cage and whips creatures at Donkey Kong Jr. to impede his rescue. Even though his revenge hasn't been sought out in the main continuity, he has done everything in his power to get back at Mario through karting and tennis matches...
Shadow Mario
Super Mario Sunshine gets a bad rap. Yes the overall idea was pretty stupid in which you jump around different world and clean up goo, but it was enough of a departure to provide an interesting take on Mario and his platforming. But I became most fascinated with the game when you notice a creepy Mario jumping around painting the world with gunk. And while the reveal of what Shadow Mario really was disappointed me and led me to more questions about potential Bowser relationships, the idea of a dark world-esque Mario hit a soft spot in my heart. He has since found a way to be incorporated into Super Mario Galaxy and Super Mario 3D Land, but not as the main force against Mario and minor differences to distinguish each version. Shadow Mario could be the Bizarro villain that Mario needs, but I guess they feel they already have that with Wario...another underutilized enemy....
Bowser Jr.'s....uh...whatever?
I really wish Nintendo would clear up everything with Bowser Jr. and the Koopalings. It was first thought that the Koopalings were his children, then his nephews, then some clones that had some extra splice to differentiate them. Then Bowser Jr. makes an appearance into the fiction and causes even more confusion. Which poses the question, what is his relationship to Bowser? If there is some creepy turtle mama out there that got the dirty on with Bowser, I would like to potentially see who that is. I see that turning out horrifically bad, so they could go the other route of him being a clone. Now, while Bowsers dark magic was able to cause the Mushroom Kingdom to be Mario's playland of killing innocent Toads and eating them (a much forgotten plot from the manual of the original game), he could have had some sort of scientist help create Bowser Jr. And in doing so, have a potential bad guy in the likes of Dr. Wily or Dr. Robotnik for the Mushroom Kingdom. Not my favorite idea, but it's still some sort of change...
Pauline
The original "princess" who wasn't really a princess. Pauline was the first love of Mario and the female who had no luck with monkeys. While she has made appearances since the Donkey Kong arcade game, she hasn't quite hit the same importance that Peach or Daisy have had. So what could possibly make her rotten against Mario? How about Mario being a "playa" who leaves Pauline for Princess Peach causing some jealous animosity between these characters. What if Pauline, who is still smitten for this world-renown kingdom-saving plumber, decides that she wants that attention back and the only way for her to get it is to remove the princess from the equation? There is absolutely no chance Nintendo would go the psycho bitch route with Pauline, but it's the one option that I'm somehow proud with coming up with.
Yoshi
Mario has put Yoshi through some shit. Not only does he donkey punch Yoshi on a regular basis, he does so to force Yoshi to eat various creatures in some awful carnivorous eating behaviors. I do believe Yoshi may very well be an herbivore as he doesn't mind eating the plants around his home. There's no creatures there, so clearly that's what they eat. But Mario don't care. He will continue smacking Yoshi on the top of the head to eat Spinies that Lakitu tosses down, he'll casually cast Yoshi off to his doom knowing there's another Yoshi egg around the corner, and force Yoshi to swim although we know he's a terrible swimmer and will die if Mario hops off. There are no characters in the Mario continuity that are treated as poorly as Yoshi. And with his fellow colorful brethren, he has the potential to overthrow (and eat) the entire Mushroom Kingdom to earn respect. And I would love seeing every moment of it.
I somehow doubt Nintendo would put any beloved characters in the villain status of a future Mario game, but there are so many choices to make it not only interesting but a huge change of pace. I'm tired of Bowser. I want someone new to make Mario's life a living hell, because he's kind of a dick. And these characters would be my choice to add some more life to the head rogue gallery of Mario.