No, it's an indication of Warner Bros poor marketing and scheduling of TMNT, with a 25 million worldwide marketing budget (and no, that's not good), TMNT was never really pushed by WB as a big time movie and really got the shaft in the wake of 300. It was released at time when the theaters were crowed with movies aiming at the same demographic as TMNT, whether it be kids or young adults, most of which had better marketing. And even though I liked the movie, the weaknesses of TMNT remain, it was underdeveloped and featured little in the way of action and fighting, points that hardly make it a must for repeat viewing.
I'm not opposed to using plots and characters from the comics, I'm opposed to the assertion that they are absolutely needed for a TMNT movie to be good and that a TMNT movie without them is automatically bad. If you were to replace the monster plot scenes from TMNT with scenes based on a plot from the comics without expanding upon them, you would get the same reaction from critics and the general audience, and may even draw more criticism from fans.
Let's say we started from scratch, and built a movie based on a plot from the comics, if it's poorly executed would it still please critics, fans, and the general audience, even if its a story they're familiar with? No. If a new story with new characters was interesting and well developed, and featured enough eye candy, would critics, fans, and the general audience be pleased? Yes, it's all about execution.
Yes, and interesting.