Might late to the party to say but terms of aesthetic, I wouldn't change a thing.
I would love if someone could actually adapted this entire series into a novel but with a heavy focus of the on-going storylines of the show and cut out all of the standalone stories or at least put all of them into a separate book of short stories like shellshocked in mirage and get rid some of the things that are just repeating each other. I seriously did not need to see three invasions in this series. I am just saying one is enough.
Oh and I would cut down on North Hampathon into one chapter instead of being 8 freaking episodes equivalent of it because
seriously just no.
So combine season 1, 2, and 3 into one big book. The change in here is that instead of succeeding in defeating the kraang in first season, they fail and it was so bad that they had to escaped the city, splinter dies, and by the time the Kraang reaches North Hampton, they attempt with a last ditch effort but fail again but at the least minute was saved by Professor Honeycutt.
The first half season 4 would be the second book ( and in this version Splinter is still dead) and later half along be the next book and season 5 would be the final book.