I don't see how them being creative and organised is a problem, aside from having two leaders who are essentially the same?
Strange about the AI being extra-friendly. I specifically tried to make the players unhappy with each other in the interest of promoting conflict - however, I did change the leaderhead file, making the AI more willing to make trades, sign pacts, etc. etc. despite unfriendliness (i.e. a lower threshold on those relations - rather than having to be friendly, the AI can be cautious) - I didn't want the fighting to make diplomacy impossible as a result of the computer being too bitter to deal with you at all.
MusX - I can't tell you off the top of my head, but the map is slightly smaller than the grid-like graphic in the first post (the scenario excludes Hokkaido). The preview shots should also give you an idea of how small it is.