Plenty of franchises are segmented. Its not particularly a bad thing. If anything, it says plenty about the longevity of the franchise when you have so many different interpretations that each have their own segments of fans. TMNT, for example, began in 1984 and since seen dozens of different takes on the franchise. Is their fanbase segmented? Hell yeah. Are they united? Not particularly. Does it matter in the end? Doesn't appear that way given the franchise is still going strong.
SEGA will never satisfy ever division of the fanbase, nor should they have to. They simply need to stay true to the franchise's roots, focus on quality, and continue to do what works. In my opinion they have been doing just that, on the SEGA of Japan Sonic Team end, since 2011.
I see no problem with fans not agreeing and going back and forth. Nearly every fanbase has that: Star Wars, Batman, Superman, etc.
What I find particularly interesting is that several members of the Sonic fanbase appear really hung up on this aspect and moan about it constantly. Sonic Adventure, Classic Sonic, Sonic Boom, Archie Sonic - they all have their fans, and the different groups don't agree! OH NO! Who cares? I find it so silly that some Sonic fans on twitter with large followings constantly talk about this. It is nothing new in pop culture.