I do that a lot. Remove weak/cheesy traits from factions and sovereigns, play as them to build up some cool unit templates, and faction ends up doing much better later on in the AI's hands.

Crap like Slave Lord, Stealthy, Diplomat, Betrayers, Familiar, Hunter gets slashed for better traits/abilities.

Come to think of it, there are only three factions that I didn't mod: Altar, Yithril, and Gilden.

Then there are little things: it's amazing how much more effective Lord Verga becomes if you add Cruel and Might to his list of traits.