An interesting topic, if I must say so myself. If I were to choose who stayed and who went, It’d be a tough call.
We’ll start with the 'Cats themselves.
I’d keep everyone, save Pumyra, Bengali and Snarfer as I’ll agree that Pumyra and Bengali were basically replacements to Cheetara and Tygra. As for Snarfer: I found him rather annoying than amusing. With Snarf, at least his loyalty and servitude to Lion-O was significant.
The Ro-Bear Berbils: I’d honestly keep them because they were not only the ThunderCats’ first friends on Third Earth, but they had their role in establishing the Cats’ Lair when they first arrived to Third Earth. However, if the scenario was in Thundera, I could see the ThuderCat Nobles appointing the Ro-Bear Berbils as engineers or soldiers, to aide the ThunderCat Nobles.
The Mutants: I’d keep Ssslythe, Monkian, Jackalman and Ratar-O because of their significance in the story arch. Vultureman, while having his uses, could be cut, primarily because he really didn’t have much of a position in the series, aside form being their engineer.
The Lunattacks: I honestly don’t see their point, save the fact they resided on the moons of Plundaar.
I will agree with Grune the Destroyer on cutting Ma-Mutt and Hachiman because while they were interesting add-ons, I don’t see Hachiman as a good fit for the series, albeit him being from a different time period. Having Ma-Mutt in the series is just as good as giving Mumm-Ra three nephews, named Mumm-Ro, Mumm-Ryu, and Mumm-Ren. Just no.
Mumm-Rana: I’d simply not even consider re-introducing her to the series because again, she was too minor of a character, like Ma-Mutt. In fact, the only way I could see Ma-Mutt working for the series if he was one of Mumm-Ra’s minions, perhaps a gargoyle. Even then, I’d save it for the rumored Rock Band series, which thankfully never came to fruition.
I’m surprised nobody made mention of Mandora, the Evil Chaser or the Zoo Keeper that had had the Mutants Exhiled.
Mandora: She would have made a better SilverHawks minor character than in the ThunderCats. While she was with the ThunderCats, Mandora just didn’t fit in my opinion.
The Zoo Keeper: Again, something I’d see fit better on the SilverHawks than on The ThunderCats. Come to think of it, I’d have to say the same for Safari Joe. He just didn’t fit either.
Captain Cracker and his Pirates: Again, they didn’t fit the ThuderCats feel. They were introduced around the same time that the TigerSharks were introduced, and I’d have to say that they’d be a better fit in Water-O, along with Captain Bizzarly, his crew and the Mantanas.
The Snarfs: They’d serve better as backstory fodder than supporting characters, to be perfectly honest - this goes for Snarf’s relatives, Snarfer, Oswald and Eggbert.
The longer the series the better