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Well, thanks for explaining the mechanic. I suppose I probably was spreading it despite not seeing the plague promotion. Probably due to me not really losing units that much there. In that particular game (epic, large, monarch) the Fremen became a beast after getting their own paradise island. I had 4 cities on a rather small island together with two angry factions when the Fremen showed up and declared war on all three of us. They had a stack of 87 sandrider blade units at one point hanging out by my city with nearly that number gain in smaller stacks on our island. They could have just deleted me but I guess the AI didn't fancy the casualties highly promoted Grenade Troopers would inflict on defence. I eventually just quit when the rest of the world declared war. I never saw the Fremen do that again in other games, they do tend to pull a bit ahead early but will sink quickly in mid-game. It helps that Grenade Troopers are a solid all-round unit for much of the game for most stacks the AI will field. I believe the AI's possibly tend to ignore building them somewhat especially when facing an enemy that also has many blade units.
As far as favourite factions go, I haven't tried them all. They each seem to be quite potent when played to their strengths. The Ecazi are certainly quite fun to play and very strong once CHOAM is in place and if you can get a few factions to fall in love with you. The Semuta Den mechanic is a great addition and fun to set up although I eventually decided it's probably more a late game thing to use your hammers on.
If you ever do find the opportunity to add things like more factions I'm sure it will be very well received. This really is a fantastic mod.