Some nuggets from an interview coming later tonight with TMNT director Kevin Munroe:
When asked about using CGI instead of live action, Munroe is confident the movie as it is couldn't have been done with the hyperkinetic speed and impossible camera angles without it. Interestingly, he also revealed that they re-created scenes from the first movie with the CGI models and in their opinion, it worked and moved better. He later added "there's also only so much emotion and expression you can get out of rubber suits controlled by servos, even though I love what the Jim Henson people did in the previous movies". As for the inclusion of those test scenes on the DVD, they're looking in to it, but there may be rights issues involved that'd prevent it from happening.
As for moving forward with a sequel, Munroe is contracted for a sequel script with an option to direct, but all that has been discussed so far are hypothetical storylines, wanting to give more time to Donatello & Michaelangelo since the other two turtle brothers got most of the spotlight this time around. Munroe is also interested in potentially bringing back the Shredder as a villain. Has also indicates a desire to dig back into the original comic series for the theoretical (though I'd call it almost certain) sequel.
He's looking to the widely-reported feature adaptation of Gatchaman next, but when asked what his dream project would be moving forward, he named two: an original comic creation of his own, Olympus Heights (Zeus comes to a small town in Indiana to subdue bad guys that keep popping up) and the DC Comics epic Kingdom Come. Kingdom Come, done in CG with Alex Ross-inspired designs, would leapfrog the problems of using franchise-attached characters like Superman and Batman, and wouldn't threaten the developing Wonder Woman property...which brings to my mind a similar route: how Marvel released their animated Ultimate Avengers movies and are separately developing live action standalone movies for Avengers characters like Iron Man.
After seeing the movie and talking with him, if anyone is going to be out there making CGI movies, Kevin Munroe treats adapted properties the right way. We should trust guys like him exponentially more than the mass-market, unfunny, condescending glut that's been CGI movies for the last few years. Supporting TMNT is good for CGI movies, supporting the other crap means letting the bad guys win.