But that is the probelm with turn based MP games, perhaps a house rule should have been in place for how many cities are allowed to be subverted per turn
I'd caution you against making too many house rules. The more house rules you put in the more chance there is that someone will accidentally break them. Also, it's much easier just to play the game with what is available than to have to consult a manual about what you can and can't do.
The problem with spies is the paradrop function coupled with the high cost of improvements and low cost of spies. I'd nix the paradrop function for spies, increase their cost, and call it a day. If you don't, anyone who wishes to go for this strategy can do so, and there's not much point not to do so in the future, as it is exceptionally effective. It reduces your scenario to one tactic, which you probably don't want.
I will make a MP version that addresses the spy-spam, and any other features you guys wish to suggest.
All in all this is a great scenario. Here are a few changes I would consider if it was mine. I'd consider these for SP as well. Only #1 is truly "MP specific," if you want to have an underdog experience in SP.
1. Strengthen the weaker civs with some useful unique units from the start like the other civs have. Consider using the extra unit slots to accomplish this if necessary.
2. Consider if it makes sense to somehow connect both sides of the map. You probably don't want to start over with placing everything but if you did it wouldn't be the worst idea to extend this the map to Panama. It would also be pretty interesting to have more territory to fight over/colonize. At least dredge southern Mexico as is often done in games.
3. See if you can do some research on how navigable the rivers are in the U.S.
@techumseh was quite correct that it's totally unrealistic for an aircraft carrier to sail all the way to Minneapolis (I think they have a draft around 40 feet and the river is only dredged to 9 at that point), but there still might be some merit to opening up the interior at least a bit for gameplay (as you said, fun over realism).
4. No one played them, but I think the weakest civ geographically in the current game (and almost certainly if you did open up the waterways a bit) would be the Pentecostal Union. Consider balancing that somehow. Maybe they're the "steppe civ" and get a little extra MP in their units.
5. You may wish to slightly tweak the effectiveness of the Raptor especially, but air units in general. We didn't have a war in this scenario but in my SP scenarios, there wasn't much point to building anything else once I had it. I think I see you added some AA guns so you might already be all over this.
@JPetroski could have used his nuke and apache to blast/capture Chicago early on. It's what I do any time I play as the Empire.
You might want to consider randomly placing each nuke in one of the cities via events on turn 1. This wouldn't stop someone from firing them first turn, but it would prevent the player who has played SP from specifically targeting the city he knows the nuke is in, which would remove the advantage from the first player to move (had I done that in a MP game, I'd argue that would be very cheesy for me to do). You might wish to do this in the SP game outright, to enhance replayability and difficulty.
I just think that rules should be agreed in advance, and not constantly changed during the course of the game. Trying to reflect a realistic state of affairs should be the goal. For example, how often do nations trade cities in the real world? Not very often. You can do almost anything with the cheat menu. That doesn't mean that it makes sense to do so.
All we did in this is if someone proposed a rule change everyone had to agree and if even one person didn't, it didn't happen, which seems to be a fine way to handle games with friends. While a few changes were proposed, I don't think we actually made any rule changes at all, unless I forgot something? Also, territory exchange has a long history in the real world and in MP games. Usually in history it was one sided and for money, but I'm sure someone like Patine could figure out some obscure time there was an actual city swap and request a unit for it
Anyway, one of my proposals was "the world is round" and you said "no it isn't," so I don't think you get to opine about how "realistic the state of affairs" was with the city swap