The amusing thing about Shredder is that he actually died in the first TMNT comic back in 1984. While he had a heavy influence in the Turtles' origin, it wasn't until he was the primary villain in the cartoon that he truly became a recurring foe for them. Then they briefly resurrected him in clone form in the comics. So it's not as if Shredder's presence is absolutely necessary.
Heck, TMNT III didn't have Shredder at all and it wasn't a problem. While that wasn't the best-received TMNT movie (though I thought it was decent anyway), it still managed to get along just fine without Shredder.
And in this upcoming movie, the Foot Clan will still be there, as will Karai, Shredder's successor. I think it's a great idea because it shows that the Foot Clan is still a threat without Shredder at the helm. As other posters have pointed out, Shredder will still have a cameo, setting up a larger role in a possible sequel, but I like the idea of the Turtles having more than one adversary, even in the Foot. After all, the Turtles are capable of making plenty of enemies.