Sega isn’t making 3D Sonic anymore. There are a few 3D bits in Sonic Colours (Wii version only) but the focus is on the 2D parts. Unleashed already had the main part in 2D, the werehog parts were 3D but the developers stated that the reason for including those parts was padding the game length. Sonic is an arcade game design, when all levels are played back to back without any repeats like you’d do in a modern hardcore game the total length is somewhere around 1-2 hours, if that. On the other hand the levels are full of alternate paths that you can only discover by repeatedly playing the levels. By trying to sell Sonic as a modern hardcore game they ended up with game lengths that were completely unacceptable.
By the looks of it Sega figured out how to avoid that problem without adding awful padding bits, Colours has you unlocking those wisp things that allow you to see levels in new light (and like 2D Mario none of them are needed to finish the levels) while 4 uses the whole episodic stuff (keep in mind that 4 worlds isn’t much shorter than the old 2D Sonic games which had 6 worlds each).
With Sega the whole mess seems to be less about developer vanity and more about incompetence. They have been making 2D Sonic games on the handhelds for a while now but they suffer from sporadically awful level design on par with the later Mega Man games (it’s not just MM9 that has instakill traps everywhere, the later X games, the ZX games and the Zero games all suffer from that).
I’m certainly not the Sonic expert. But I remember being disaponted by the Sonic handheld games (the DIMPS ones). Incompetence? I’ll agree to that!