Episodes which SHOULD have happened but never were.

[The Great Saiyaman]

Let's imagine that we can write a sixth season and have it about unresolved plots and background stories.

- Kraang Prime
What happened after the events of "Annihilation earth" Kraang Prime never appeared in the series after that, apart from being mentioned in "The war for Dimension X" No explanation what happened, did he die at the hands of the Triceratons, or did he survive and bided his time to unleash something like...I don't know... a giant mutagen bomb?
So there should have been an episode which shows Kraang Prime's history in more detail and what he had been doing since his final appearance.

- The Pulverizer.
At some time after the events from "The invasion" the container with Timothy is empty, what happened? Did the Kraang when they came into the Turtles' lair went "This container which is known as the container which contains a being who can be of use to what is known as scientific reasons to Kraang." and take him with them?
In my own personal head cannon, I'd have Donatello contact Bishop and have him take Timothy to dimension X and restore him using Kraang cloning techniques and plan 10 technology to transplant his mind from his mutagen man body into a new body. It would have made for a cool episode, perhaps the Utroms could have trained Timothy so he could have been the Hero he wanted to be.

- Kraang Subprime
"The war for Dimension X" revealed a glimpse of his past, how he was a part of the Utrom Council known as Knight. So what is the deal, how did Kraang Subprime became corrupted, what made him turn into the vicious, battle scarred warlord?
There should have been a special of several episodes long which shows what happened, how Knight and Bishop were friends, how Knight became corrupted and Turned into Kraang Subprime. I imagine that Kraang Prime, having gotten a member of the Utrom Council under his control would have made such an awesome "Darth Vader" moment in the series. Heck, why not an episode which shows what happened with 87 Krang and why Subprime banished him to the FW dimension. Or what happened to Subprime in the Mirage dimension, the Mirage story lines does have Utroms.

- Karai
Of all of the henchmen of Shredder's we know the most of Karai but we also don't know all that much. What kind of childhood did she have, did she have a mother figure growing up, what kind of father was Shredder to her, how did her training with Tatsu involve and how did she meet Shinigami?
But in addition to having episodes which answer those questions, there also should be one which shows what happened after she mutated, we know that the Turtles searched the whole city for months after it happened trying to find her. Perhaps an episode which shows us the events from her point of view, how she hid in the shadows, going from full snake to her in between form to keep a low profile, learning how to survive. A Key scene in "City at war" was when she transformed to take on Tiger Claw, her body convulsing as if she's going into a grand mal seizure, signalling that the change must have hurt severely. Perhaps the episode could have shown that she realizes that she stood a better chance at survival if she stayed in full snake mode.