Try not to get sad over Arne not finishing a project, I've just been to his homepage and I figure he does this a lot.
I agree with most of this reimaging, bar the ancient toad robots because I refuse to believe Mario needs precursers the way Arne does about every game.
I like the idea of goombas being spawned from thrown seeds or something. Perhaps they can shout to the koopas when they see Mario, thats all the use they'd need. They are the front liners, just there to wear Mario down and alert the koopas. It would be funny if the koopas abused them, like spawning one just so they can jump on it to get to a higher point.
Koopas I don't have much to say about; soldiers. Oh, I would add that if Bowser is a koopa, in theory any powerful koopa would have a spikey shell and breathe fire.
Shyguys interest me more, if you've played Yoshi's Island you'll know why. These guys are great inventors and are even more all purpose than the koopa, with flyguys, stiltguys, candleguys and many more. If I was to roll the designs togethor I'd say they're related to the boos, as in they're ghosts in special containment suits.
The princess needs to be a mushroom person too, if we want to make sense. Or we add more humans to the world and rework Mario's history. I will say Mario the Italian American will always be the backstory for me.
One last thing: items should effect enemies too, if you let them out of your grasp. Imagine a starman hitting a lowly goomba and turning it invinsible for a time.
Thats what I'd do anyway, carry on!