Just don’t replace 2D with 3D. The 2 aren’t interchangeble. You’ll always get a sort of hybrid that sticks out like a sore thumb. (Hence my comparison to the Rescue Rangers trailer.)
CMI’s whole look is based on hand drawn animation, and it works because of it.
If you want to remaster, use 2D. If you want to remake, build a whole new game and make it fully 3D (or claymation for all I care), but don’t use any of the original assets and reïmagine the whole project from ground up.