The fracturing of the fanbase will happen. No matter the changes done to the system. Minor or major. Paizo can attempt to minimize the effects. To be honest I think it's a waste and they should focus on developing the rules and playtest. Even with PF being similar in ways to 3.5. their still is some that play that edition and only that one.
Unless their is a significant and large amount of gamers who uses 3.5. material at their table I don't think the next edition has to be backwards compitable. It would help but if only a small portion of the community uses older material it should not be that big of a priority imo.
Paizo is kind of in a difficult position imo. Release a rehashed edition and not sell as much. Release a new edition and that too is a problem. Competition from other rpgs.