I thought of what the game should be about. A villain ( Haven't thought about it.) kidnaps the 7 Koopalings including Bowser Jr. Bowser then has to save them. You can use him to shoot fire, jump and punch. You rescue one Koopaling each time you defeat a boss.
The bosses could be the mushroom people or any recruits Mario could get. Heck, Mario could be a boss a few times that escapes when defeated in all but the last level. As for the order in which the Koopa kids are rescued, I don't think the order should matter.
I got it! Boss 1: A muscular Fire Bro (You rescue Iggy) Boss 2: Midbus (You rescue Morton) Boss 3: Goomboss (You rescue Lemmy) Boss 4: Petey Piranha (You rescue Ludwig) Boss 5: A giant Wiggler (You rescue Roy) Boss 6: Ice Midbus (You rescue Wendy) Boss 7: Luigi (You rescue Larry) Boss 8: Mario (You rescue Bowser Jr and beat the game. But,you fight Mario in many phases. Phase 1: Normal Mario,Phase 2: Fire Mario,Phase 3: Raccoon Mario,Phase 4: Normal Mario but he uses the Power Stars in certain times,and Phase 5: Mega Mario) (Ending: Bowser triumphs over Mario and says "YES!!! YES!! AFTER MANY YEARS,I FINALLY DEFEATED THE MARIO BROS!!!" He then walks away into his Koopa Clown Car and flies away to plan to capture the Princess another day.) The worlds are like this. World 1: Bowser's Kingdom World 2: Desert Dunes World 3: Mt. Goomba World 4: Piranha Jungle World 5: Uncharted Forest World 6: Frost Land World 7: Mushroom Kingdom part 1 (The neighborhood of the Mushroom Kingdom) World 8: Mushroom Kingdom part 2 (Peach's Castle)