I'd have to mention the Donkey Kong Country property.
The SNES games used rasterized CGi pixel art as we all know. It also had a style though, outside of just being computer generated. When it made the leap to the Wii, that 2D style was thrown out the window and replaced with 3D models. At first, I was hoping they'd have used 2D graphics, something more akin to the newer Rayman games, but at the the same time, there really isn't a way to effectively emulate that particular style that was born out of such an odd place between bleeding edge tech, and aging hardware limits. Any attempt to mimic that pre-rendered style may have looked awkward, imo. So the leap to 2.5D made the most sense.
I think the Returns games look and play great, but a small part of me wonders what they would have looked like with the old style. To be fair though, I don't think Tropical Freeze in particular would have been as good if it was locked to two planes. I know this sounds weird, since I've said before that I don't like 2.5 graphics that much but in a game like Tropical Freeze, it manages to make the level design even better, cause they actually do something interesting with that space. Games like Samus Returns, or Cave Story 3D don't need to have 3D backgrounds, cause they don't use them in any meaningful way.
I typed up this post really fast, and I feel like I'm forgetting something else, but g2g.