All they need to do is make Metal Sonic a persistent threat. Combine upgrades being given to counteract the methods of defeat multiple times through the film with the terror of persistence predators and you have a solid opponent, especially as the group underestimates Metal then realizes "Oh hey, this might actually be a problem this time".

I just want to respond to the "it has -never- made sense for Gerald Robotnik to bio engineer alien dna into a fecking hedgehog while trying to develop a cure for Maria" part here.

-Maria wasn't his only project/point of concern

-Gerald, at least as the lore has been expanded upon, found the prophecy on Angel Island (the same one Sonic and Knuckles fight in front of in the game of the same name, back on the Genesis) and that became the core of much of his work

--I personally believe they always planned at least some of that, given the similarities we see between Angel Island and ARK