I almost forgot about one of my favorite clones ever. Vexx. It was made by Acclaim in the early 2000s. It was literally a Mario 64 clone in all respects except the setting.
The game was dark and moody, but the gameplay was
literally Mario 64. It was like they said "I love Mario 64, but it's way too kiddy. We need something for the adults to play!"
It had the large sub levels with 7 stars to find in each. (Replaced by beating hearts that actually vibrated the controller as you got close to them)
All of Vexx's moves were copies of Mario's except for a single one, the long-jump, which was replaced with an uppercut move. But the rest were there. Triple-jumping, crawling, punching, diving...
It even had a level that was like the church in Mad Monster Mansion in Banjo-Kazooie in that it was a living room, complete with video game console and TV you had to play and a piano, but it was huge, or rather you were small. Well no, it was huge. I think it belonged to a giant or something.
Unfortunately it didn't have a hub level like Peach's Castle. Instead it was a non-navigatable circular room with doorways to each level.
It also had its own day/night gimmick where you could change the time of day in real-time.
Unfortunately it did not rip-off Bowser because the final boss was impossible as hell. I couldn't lay a single hit on him and gave up after a while, but I pretty much 100% the rest of the game and was so disappointed at the final boss. I even tried following a walkthrough. I could not hurt the boss.
Personally, if it were even possible, I'd buy a PC release of this game just to play it again. Unfortunately, Acclaim doesn't exist anymore and I don't think anyone even bought the rights to the Vexx brand, even though at the time of auction, it only cost a measly $5000. I owned it on Xbox but wish I'd had the GameCube version instead because I'd be able to just play it now. (My Xbox and PS2 don't work anymore. But my Cube does.)