I'm aware of the controversy on the patrol issue and will be fully reading over the other topic again. Up till now I've basically just ignored it but I ought to make a decision one way or another on it.
Ouch, I've posted some really long posts in that thread. Good luck!
By the way, I just remembered another bug that I've never seen mentioned by someone else (although I haven't read every single post on this site) but which I think is pretty serious and basic: the aerial reconnaissance mission bug.
When you're exploring with normal land units, then units on high terrain can look over low terrain to see tiles on the other side of the low terrain (and can see high terrain behind low terrain). The various rules governing this process are not too difficult but would still take a lot of time to explain in detail. While this is perfectly realistic for land units, I personally think it's utterly ridiculous that a plane exploring over sea tiles can't see inland tiles while a plane exploring over land tiles can see many tiles into the sea area (and similar ridiculous situations).
I'll show some of these situations with some pictures as a picture is worth a thousand words. Note that the normal aerial reconnaissance range is rather huge, but the terrain factor can be debilitating.
My suggestion would be to make aerial reconnaissance viewing range independent from terrain.
1 Standard Reconnaissance Range.JPG
2 One can't look from water to land.JPG
3 One can't look from water over hills.JPG
4 One can't look from flatland over hills.JPG
5 One can't look from hills over mountains.JPG
6 Forests don't help with the viewing range.JPG
7 Flying over a mountain is the best.JPG