I've been playing MGE for many years, mainly due to scenario requirements. Also I played normal civ before I discovered MGE here, on Civfanatics around 2004. Main differences would be just like you said, extremely hostile AI. Also there was an annoying bug with being unable to close city window, and I had to kill the process in task manager. It's fixed in MGE. All other rules and game mechanics seem to be the same in both versions, except possible map size being larger in MGE, allowing for really big world maps (mega or giga world is the name IIRC). The problem with cheat menu is also interesting, I've had situations where for some reason my cheat menu was active from the beginning of the game. I could cheat as much as I wanted, then CTRL-K again and the menu deactivated. When I tried to activate it again, it said I would lose the score if I activated it. Upon reload, sometimes the cheating menu was active again, sometimes it remained inactive for the rest of the game (or until I activated it and lost the score that way)
Now, if I kept the menu active and only turned it off a turn before the end of the game, by any means, without reloading, my score would be just fine, no penalty for potentially using the cheat menu.
Although if done properly it could be an interesting way to cheat, and undetectable as well, I believe it can be annoying at times, especially since my cheating days are long gone, and achieving a 100% fair and legal victory is more satisfying than nukes in 4000 bc... plus it has a way of tempting you, when you see those damned Zulus are gonna build Leo in the next turn and you need at least 3.
Another thing of which I am unsure is internal AI intelligence. I think it's been improved in MGE and during wars between AI civs now, there's a chance of a civ being destroyed. I played once on MGE and Zulus, having settled in Africa, took over entire Mongol civ that spanned over 80% of Asia. It was on giga world I mentioned before and the year was around 2400 ad. Never happened to me in classic version.
EDIT:
Another difference I just remembered: There is no gold limit in MGE. I've gone over 2 million gold in some games and no problems ensued, other than the price of enemy cities as well as some gold-based diplomatic options have grown according to their wealth. Worst thing was, the enemy AI still only offered 500 gp if I agreed to attack someone else. Imagine 2 bil gold increased by the astounding amount of 500. I've had MGE games where cities cost over 600k and asking to attack an enemy civ cost around half that, peace treaty/cease fire agreements float at around 100k. I still have a screenshot:
http://img4.imageshack.us/my.php?image=civ2ek7.jpg
It was an MGE scenario with alien visitors, 1vs1 - me vs comp AI. I've no idea how much gold did they have, it must have been at least a couple times more than me. Although you all seem to finish your games early, so extensive enemy wealth shouldn't be a problem for you, it's still worth noting if you plan to play for fun into later games.
In case someone is interested in other modifiable game mechanics, it seems that at least 2.78 version of classic civ and MGE both use the same rules.txt file and I just found out they are mutually exchangeable. I have those 2 versions as well 2.42 on my HDD so if anyone is interested I can provide any comparison between them.
. Last time i built Marcos, (gotm 94, emperor, one city) the turn i got it, i couldn't get a single tech, even with multiple giftings... and forget about maps 
. After placating one guy and making peace, i tried to trade techs and he said "all of our great minds are busy working on our glorious project the Pyramids. Perhaps we should speak again later". This guy was gifted to worshipful and i kept getting the same response. And maps? A worsipful civ tells me "we have no use for your feeble maps". Does this happen with original version too 
Is this something that occurs in classic version too... or does classic provide a safe haven from the unfortunate capability to cheat?
