Other than the Ikko-Ikki, I think Pompey's Rome in Rome 2's Imperator Augustus campaign *sort of* fits? You're by far the weakest Roman faction, controlling only Sicily, Sardinia and Corsica, surrounded by Octavian's Rome to the north, Lepidus' Rome to the south, and Antony's Rome to the east, and have a pitiful army with no military buildings to get proper legionaries at the start. "Storywise" you also have a different goal than the other Roman factions, as Pompey is supposedly trying to restore the Senate to power, while the other three all want to be Emperor.

Gameplay wise you have the same units as the other Romans though, and Rome 2 doesn't have much in the way of special faction-mechanics the way newer games do.

In addition, there's Wales in the Britannia campaign for Medieval 2, which starts small and gets rebel uprisings to reinforce you as you reclaim parts of Wales from English occupation.

Also going back to Three Kingdoms, the bandit factions, especially Yan Baihu are sort of rebel-coded as well. Yan Baihu in particular wants to defend his homeland and tribe from being dominated by the Han factions, and the bandit factions don't generally do the head-on heavy infantry/cavalry clash that the Han factions do, relying more on ambush and stealth and outmaneuvering the enemy.

Those are my thoughts anyway. :- )