So here's how I'd like to see Nintendo setup the next main Mario game:
Bowser has disowned the Koopa Kids for not being able to help him stop Mario and basically boots them out from under him completely abandoning him as he returns to his home lands (think Super Mario Bros. 3 World 8). This is when Bowser Jr. shows up to recruit the Koopa Kids after he himself was disowned by Bowser for similar reasons.
Together all eight of them overthrow Bowser and take over his kingdom. It doesn't stop there as Bowser Jr. has a plan which doesn't involve taking over the Mushroom Kingdom but instead expanding the existing borders by spreading fire and lava. Each Koopa Kid is sent to a land (Mushroom Kingdom, Sarasaland, Del Fino, and so on basically revisiting major areas from past games and using them to inspire the level design of said world) with a fire crystal which, once activated, causes a volcano to grow and erupt spreading lava and fire across the land converting it into perfect territory for Bowser Jr.'s new empire and making the land unlivable for the prior inhabitants.
Each time you clear a level within a world the level design will slightly change (think Super Mario Land 3 with how levels would change as the world itself changed) with fire and lava slowly spreading. For example in the ice world the ice will obviously melt and be replaced with more a water level that will rise, some platforms will be weak and collapse under the weight of characters, you get the idea. Other areas will become more hazardous in their own ways as this effect spreads. Worlds will also have several paths through them and once a fire crystal is destroyed the land reverts to its original state and all past levels can be revisited.
Bowser meanwhile seeks the help of Mario, Luigi, and Peach to stop Bowser Jr. and the Koopa Kids from ruining his land and keeping the true king from his rightful throne. The three agree to help him (or rather stop the destruction of the surrounding lands) and team up with him. Mario is the balanced character. Luigi is about speed, slippery controls, and high jumps. Peach obviously has her slower jumps, hover ability, and isn't quite as fast as Mario. Bowser is slow but powerful, he's able to use this strength to one hit enemies Mario and the gang have to hit several times (like Chargin' Chuck) and can also breach walls and obstacles no one else can (think like Knuckles from Sonic 3 and Knuckles) which opens new routes and secrets on levels.
The game ends with Bowser Jr. and the Koopa Kids being defeated but swearing revenge, not just on Mario and friends but also Bowser too who admits to being a bit too harsh on them and basically apologizes for his actions so they can make up. As they bury the hatchet they basically come up with the idea to attack Mario and them which is where the game leaves off with Bowser, Bowser Jr., and the Koopa Kids laughing evilly while Mario, Luigi, and Peach look on nervously wondering if they truly made the right call with Bowser.
