Plus, most Indie titles are made off on engines like UDK and Unity anyway, because all the insanely hard work has been done already. This would be the case where you have a single guy with a vision but little money attempting to make something cool. However, for game companies like SEGA, you have multiple divisions working together using their own skills to make a game; these people would be artists making the level geometry, level designers making the level layout and topology that the artists make their high quality art around, the programmers that make everything able to actually work, etc.
Basically, if you're going to be making a Sonic game up to par with any other indie titles out there, the last thing you want to do is rush into making one entirely on your own. Don't be afraid of help if said help is reliable
That said, this idea of a fully customized engine built from the ground up for the persuit of the perfect Sonic engine is intriguing, and would be interesting (nay, amazing) to see come into full fruition(sp), but I have the stinking suspicion this would turn out to just be a grande theory. Don't get me wrong, I love the idea, but considering how much work would have to be put into it, if you have the skills you might as well make your own liscencable engine and make a unique game for it... Which is exactly what people with this kind of skillset do.
Of course, if you do end up doing exactly that you can of course allow free liscencing of the engine for noncommercial open-source use (though that may be risky) and give the engine the toolset you need to make a great Sonic engine / game not as an indie company, but as fans.
...what's more is that when you get to that point, you can likely strike a deal with SEGA to develop your own unique Sonic game in your own vision and sell it, if you're lucky. After all, SEGA liked Taxman's work enough to liscence his engine and remake Sonic CD, didn't they?