The idea that the blue kraang are a halfway house between the 'Normans' and the plain kraang droids is interesting. Hadn't considered that...
Although the idea that the human ninja are simply dismissed is a nice clean explanation in one sense, it does then open up the question of how did they keep them quiet - which leads to some pretty dark answers. I always thought it would be cool if they were forced into some kind of cyber conversion to make them into learning cyborgs - but I'm not sure thats any less dark.
Certainly if we're surmising that the other scientists the Kraang captured were just killed/mutated off screen that really does nothing for the off screen grim darkness that hides behind the on screen antics of the show
Interesting count for the mutagen canisters! I guess that at least clears up that question - though personally I always thought that The Foot or the EPF had gathered up the others.
As for the Footbots and other villains growing easier as time went on - again I personally put this down to a nice visual way of showing the turtles getting progressively better at fighting and learning the weaknesses of their regular opponents as time progressed.
One thing I did notice as well from a rewatch of the first couple of seasons is just how often they talk about time passing in 'months'. This may be down to some exaggeration, but even then it rather implies a significant length of time passing in each season. I'd always assumed it was about 1 season = 1 year but I know there were people on the forum who weren't convinced of that.