Some random thoughts....I think the Great Rebellion can be a blanket for a lot of the good guys to fit into.
If you did Preternia people like: Black Bird, Birtha, Hero, Hiproar, Terror Dac, Spyfly, Rillo, Megetor, Tytus would fit in.
Etheria sub groups I can think of would be: Twigets, Manchines (manchine man could fit in there as well as his 5 ani-manchines) and the villian ones could be in there too... can't remember their names right now, Sorcerers ( Castaspella, Frosta, and the lot of one shot villian casters), Bright Moon (Queen Angelica, The Red Knight, Glimmer, Gaurdsmen), If you did a great Rebellion group you could include in it people like the dad from the missing axe or other human rebels who stuck out, Etheria seems to have less defined groups though other than Rebellion and Horde.
Maybe you could devide the Horde tour into subsects/part. Part one Horde females, part two horde men... or just have them random but in 3 or 4 parts, where in each part you'd feature 2-4 headliners like hordak scorpia catra grizzlor, 2-4 not as well known characters like Batros, or one of the Generals, and 2-4 horde fan characters.
I think a Comet Warrior tour would be cool. You have the three from the toon plus like 30+ fan ones to choose from.
Sands of Time tour could be cool too: Charmor, Shehara, Rain's Sandra, SMB's Kactura, and then all the filmation sand people.
Again these are just random thoughts.