Well, they kind of needed to defeat it in a minute. It kind of eliminates the possibility of a Big! Climactic! Finish!, unless you go the Dragonball Z/shonen anime route and decide that 1 minute actually means 1 hour.
Kids today; if a villain doesn't destroy the whole world, it's not impressive. Consider all the large scale economic transactions that weren't completed or were delayed because of the transformation, or all the V.I.P's--starting with, possibly, the mayor--who may have been killed by the demons. Think of how 9/11 changed the world, and multiply it by a factor of a hundred--that's what the Shredder has done, without even a shrug.
Now, all kidding aside, I definitively get what your saying--I find the season dissapointing too, at times moreso than Fast Forward was, and while I have a definite idea why that is, I can't really express it. Part of it is pacing: the whole thing suffers from both being too long (there's not enough story here to justify 13 episodes) and too short (we've lost two thirds of the season's cast before we ever really got to know them). Part of it is the difficulty of having an antagonist much stronger than the heroes without having him be unbeatable. Yet another part is the Naruto-style super-moves--which tend to land in the wrong side of the line dividing "cheesy" and "cool". And then there's the feeling that they're making this up as they go along.
Still, there's been a lot to like about the season. I've liked most of the new characters (except for poor Tora, who's been especially underused), and there are a lot of cool moments. It's just not as good as it should have been.