Having played a couple of games of HW through (and starting a far greater number!), then gone back to Civ4 (with AdvCiv) - I do think this mod is absolutely great. The civics, religion tenets, use of combat mechanics (retreating particularly) feels like this is how Civ4 should be.
I have a few things:
It seems easy to skirt around the civil war/dissent mechanic taking all the units in the revolting city by just evacuating them completely once they become rebellious. It's fun to play around but it feels like a 'gotcha' if you happen to have a big stack garrisoned, and it doesn't seems like the military stack does enough to prevent a rebellion, even if you can see it coming a ways off. There's even the loading hint pointing this out. Wouldn't it be better if you didn't have to do this manual micro? Maybe if you have a stack in a city which rebels, they should fight immediately, and the city should lose some population if the rebels lose.
There's a general issue with lategame slowdown and stuttering, not sure what from. Feels it correlates with ships/water, and seems to have decreased once upgrading past clippers.
AdvCiv incorporates a mod where when looking at building options, it says what the effective change would be (so if you're running the right civic/have the right resources it'll say +2 happy faces etc)
E: apparently this is the "absolute building effects" part of BUG from the city screen tab of its options, but I can't see a BUG options menu in HR, despite it being incorporated...