First off, the obligitory: "Wow, what a great mod. Congratulations, Kael!"
Secondly, I'd like to state that I'm one of those "The only Civ IV games I've won, I've won with cultural/diplomatic victories" that naf seems to think are in the minority in this thread (and, actually, I probably agree with him).

I wouldn't exactly call myself a "peacemonger," but I'm definitely no warmonger.
War Weariness: Since there is a clearly designed axis of good/evil in the religious system of this mod, is there a way to significantly reduce war weariness when you're fighting civs of opposing religions )and maybe increase it for intra-religion fighting)?
Civics: I'd agree that some of the civics could use a little tweaking, but I'm at work, so I don't have them handy... Maybe I'll get a chance to look at them more closely next week when I'm on vacation (yay!). Offhand I remember that Pacifism's GP % was lowered, which I found a bit surprising, as I never really found it unbalanced in vanilla... though you did add several more categories, which could multiply imbalances... anyway, I'm rambling! I'll try looking at them and give my 2 cents, along with everyone else
Production: I haven't seen anyone else mention this, but production seems significantly lower in FfH than in vanilla, partially due to pushing forges way down the tech tree. Granted, I've only played a couple, very "unfocused", games so far, so I may just be mistakenly skipping the techs with production boosts... but it was something I'd noticed.
Religion: The couple games I've played were just Noble so far, but both games I got all the religions, without specifically intending too (I was just jumping around the tech tree, going for the next "cool" sounding tech - figuring things out, basically

). I had to send different people different religions to make things interesting

Aside from me ramping up the difficulty a bit, is there a way to maybe prioritize the religion techs a little more?
AI: Yes, it's been mentioned, already. However, 200 turns into the games, I'm still finding most AI cities are guarded with warriors (with maybe an occasional hunter). I tried popping into the worldbuilder to see what kind of buildings they have in their different cities, but I'm not familiar enough with the new buttons that that was just too much of a chore, and I wanted to get back to playing with my new toys!

If you're looking for input from more digging into that sort of thing though, I'll dive back in. One (mostly untested) theory is maybe the AI doesn't reconcile the building requirements and the resource requirements at the same time very well? (i.e. they're building barracks, but don't have the copper needed to build axemen... or they have horses, but don't understand that stables are needed, too, etc.)
Baron von werewolf guy: Wow, he's cool, but seems pretty dang powerful. I turned him and a couple medic friends vs raging barbarians into a potent werewolf army in just a handful of turns. Maybe tweak the "create werewolf" power to work more like command (50-75% of the time they turn, instead of every time)?
Barbarian scouts: Ouch! They're evil little worker killers. I love them. I wonder though, does the AI protect their workers as well as I've learned to (the hard way)?
I suppose that's good enough for a first post

I'm looking forward to playing a little more this week, and even moreso to v1 and Phase 2! Congratulations (and thanks!) again on an innovative and entertaining mod!