Dearmad,
I like you MOD because you have deep understand of the gameplay and done a great job, it has deep consideration of gameplay and get some remend of AI weakness, and i am willing to contribute some idea to help the MOD. I think a good MOD should always help the stupid AI relative smart for gamplay, that's the key.
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the lighthouse:
maybe i'm not native english speaker so i had not speak clear, not said you had mod it, just a suggestion idea:
a single tile island in ocean should not go to 25 population for less attrative for human player, and in the ancient age, fishing should only available at coast. and if lake in the city area, the lake also look as "sea" getting benefit.
check the XML, lighthouse bonus "seaplot" - that means all water, don't know could realize this idea by changing "seaplot" to "coast"...
if reduce the effect of lighthose to just coast, even a single island, the benefit wil be at least 8 coast area surround them, to feed this island up to 10 population with the reduced lighthouse... and with a fish +4, it could raize to 14 pop.
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settler in jungle/tundra(maybe include desert?):
maybe should set settler could not settle (or not enter, maybe it will help AI not explore a big jungle in Earth map?) in jungle/tundra in early age, the idea of MOD just prevent the AI and player expend to bad land too early, maybe a tech later in medieval age could make this available... if playing the 18civs Earth map, this setting is good for no early settlement in jungle/tundra/jungle filled island for better realism, how about mechineary (or ironwork? seems a little early but more realism) to enable them settle down?
another 2 idea of gameplay and helping AI:
ideas of razing cities rule MOD:
http://forums.civfanatics.com/showthread.php?t=139511
idea of population cap MOD by ages:
http://forums.civfanatics.com/showthread.php?t=139518
another idea is fast moving army (cav/tank) should not enter jungle (maybe include iceland) but it may damage the AI?