1. Northampton- After dealing with The Invasion (arguably one of the best episodes of the series), this is what we deal with? Primarily horror tributes in a changed environment?
While I prefer horror over sci-fi (I'll get to that soon), the change of location made season 3 really slow paced until Battle for New York, where the Kraang issue was squared away. What could've been a great opportunity to build character and emotion just turned into a monster of the week I expect out of an old superhero cartoon.
Something that should've been done is bring the episode length down to 7 or 6. Keep Buried Secrets and In Dreams, I felt those were the best of the seven horror episodes. Use about three episodes to build on issues the character face (I would say Foot Too Big could apply if you wanted). Then, maybe an origin for the Mutanimals instead of just an Amazing Adventures comic (I still think it's non-canon) and finally a two-parter on Vision Quest. Move Bebop and Rocksteady to midway in the season though, focus on the Kraang first to get them out of the way, preferably permanently.
2. Mutagen Man- As constantly mentioned, the bit of evidence we've heard is "He'll play a role in the second season" and then he only got one episode, Mutagen Man Unleashed. More than likely it's due to Roger Craig Smith, his VA, who does various cartoon roles such as Sonic (both Sonic Boom and the games), Captain America, and more.
Mutagen Man did offer a different dynamic, even if Timothy was among the weaker of the new characters introduced in this series. However, I almost feel that had the season 1 team stayed, he would've been an active force. I always thought he'd be the reason for the creation of retromutagen, possibly even being a sacrifice if he wasn't going to stay.
I'm not sure if Mutagen Man was extremely popular with his toy in the FW days (can someone verify?), but he held almost no purpose. He could've helped Donatello grow, but otherwise, he was fodder to the bigger picture of season 2.
3. Slash and Newtrailizer- I put these two together because both suffered a similar issue. Both of them started off as badasses, but then after Newtrailized!, they changed. I'm not sure if writing or because of contracts, but it felt questionable.
To begin, Slash. His debut in Slash and Destroy was awesome, probably one of my favorite episodes of the entire series. Following it, Slash's turn to the good side was a bit forced. Obviously, there's the example of "The mutagen warped my brain," but the change was out of nowhere. What could've been an intense rivalry between pet and owner/family and it turned into a simple goodbye and then changing his allegiance? I wish it were more gradual.
As for Newtrailizer, his expansion stems from appearing minimally. It keeps him from being overexposed as the Kraang and instead like Rat King, where things would go down when he shows up. The problem I have is there was a golden ticket during the space arc to bring him back. It could've been a fun dynamic to serve as an anti-hero for a bit and later betray the Turtles and his people. I've yet to watch When Worlds Collide, but I did read he teamed with Dregg. I just wish he was used a little more, especially because season 4 was perfect to use him.
4. Mind Control Serum- What was the point of this? Prolonging Karai becoming a full-fledged ally to the Turtles after her mutation. It took up the majority of season 3's second half with some exceptions (Mondo Gecko and the Triceratons mostly). Despite hinting at the Triceratons, I almost felt their appearance dampened the end of season 3; they raised the stakes but didn't fit in with the rest of the season.
For the serum, there are two things that happened: Karai remaining a slave and Raphael, Slash, and Dr. Rockwell being test subjects for an episode. I'll start with the former. Despite the imagery featured in Attack of the Mega Shredder! and The Deadly Venom with forcing the worms into Karai, using this felt convenient and at the same time rough. Convenient because it can keep the stakes up for Shredder and Splinter's feud. Rough because they were so many possibilities following it. Karai could've attacked the lair in a home invasion, she could've kidnapped Splinter (even if done before), there were different scenarios that would've made some suspenseful, even horrifying, episodes. Also, healing hands.
As for "Dark Raph," I really don't have much to add to it. That story ties directly into season 3's biggest faults: its pacing and especially the storytelling being more all over the place. I almost felt like the story could've been two parts or even at the end of the season instead of the Triceratons.
The story I would've done is this: Raph is feeling bad for Splinter and Leo about Karai and decides to team with the Mutanimals (or Mikey and Donnie) to break her free. However, Raph gets captured during the rescue and is subjected to experimentation. Then you can hide him until the end of episode 1, glimpses of his training and shock everybody when we see him gone rogue. Mikey could then break him free as a callback to The Invasion, Karai's story could end strongly, and it could be the end of Shredder for a bit of time. It also lessens the impact of Splinter's second death in Requiem.
I'm not sure how to fully rebook it without changing season 4 drastically, but that's a concept I would like to play with.
5. The crushes/relationships- Most of them are downright putrid and one of my least favorite aspects of the series. Not enough clever or witty writing to make them engaging and not enough chemistry for me to buy into it either. This applies to pretty much every relationship except Leonardo and Karai (until Broken Foot, at least).