I've come across a couple of problems so far in my most recent game:
The main issue is not your fault, jdog, but rather something that should've been tweaked in the regular game that when combined with the Revolution mod really just makes the game a total nightmare in my opinion.
The citizens don't seem to draw any distinction between being attacked and launching an attack against somebody... consequently, I was playing and I was attacked by Montezuma, and the unhappiness is a dozen core cities suddenly went from barely nothing to raging as I had anywhere between +7 and +12 unhappiness from war weariness. Now, if I had attacked Montezuma, perhaps that would make sense, but even then that's a bit extreme for it to happen in such a short span of time... but I didn't... I was the one who was attacked.
As a result, one of my highest producing cities went into rebellion and a massive army spawned right outside it and I had to evacuate and let the enemy take it or else sacrifice the units inside. That only worsened the problem as it encouraged others... I stamped out the rebellion there, recaptured the city, and ended it. But not two turns later and one of my other core cities rebelled and that just produced another large, high-tech rebel army outside another main city.
Keep in mind that half of my commerce was already going to culture to try to make use of my Colisseums and Theaters... and I had almost every luxury resource with Markets and Forges and several wonders that increased happiness in cities and STILL the cities were unhappy enough to rebel... And I don't know exactly what the factors are for the civics, but I had some very population-friendly civics...
So I'd say that the war weariness DEFINITELY needs to be tweaked so that if you are the one attacked, the war weariness will take considerably longer to appear and certainly take a while to become out of control like that.
Some other minor criticisms and suggestions are:
There really needs to be some kind of special unit for rebels that is not quite as strong as the regulars. I mean, to suddenly go from having nothing to having a large, fully-equipped army right in my heartland (which in a foreign war is usually my least-defended area) is not fun... it's just annoying. In fact, I'd rather have portions of my military defect to the rebels rather than the rebels just getting these high-tech free units from nothing... I mean, at least then, you increase the survivability of the rebellions while having it seem a bit more reasonable.
Also, there's really nothing I can do about rebels except destroy them. I can't negotiate. I can't switch civics to placate them. Once they're there, they're there... As it stands, the rebels just form a new country... which considering that they're ethnically a part of my civ and have been since they were founded, doesn't make much sense. I wouldn't even mind getting ousted from power... at least then the civilization would go on as strong as it has been and not be crippled by being divided up amongst rebel factions.
I'd like it if there were some kind of grievance that they wanted corrected... That's why rebellions happen often anyway... they capture an important city and then the national government has to take notice, negotiate, or try to obliterate the rebellion. And considering that that those horribly inconvenient rebels had me by the short hairs, I'd have dealed
Seriously though, demanding me to change civics, make peace with a foreign enemy, or agree to some other demand would be good ways of letting me stay in power.... because sometimes I just don't have the money to pay to keep them quiet and so I either have to turn my armies around and head back to a main city, or JOIN the rebels... and I certainly have no interest in doing that. Forcing the civics changes and peace talks if I'm completely overwhelmed by the rebels would work fine too. It depends on their goals... sometimes they are just separatists and in that case the status quo is fine.
Also, the fact that I crushed one rebellion didn't seem to deter others from starting... seems to me that if the rebels capturing a city should encourage a wider rebellion, crushing one rebellion should discourage new ones from forming right away.
I like the fact that sometimes you get prompts telling you that a rebellion will be happening soon, but it seems somewhat inconsistent... sometimes I get a prompt, and sometimes I don't.
But considering that my previous game didn't even have a single rebellion (because my wars were short, sweet, and very infrequent) just tweaking the war weariness would be like night and day because I really haven't been the one starting these wars in the first place.
Glad you enjoyed it.
