MASSIVE Props to the OP for creating an extensive to-do list for Col 2 modders. Yes its a harsh review of a game I happen to like, but it highlights some of the major areas which do need improving.
I think that Snoopy/Dale's PatchMod addresses some of your complaints already, particularly points #12, #22, and partially #24 (no more indians training in their own villages) which for me seemed to be everybodys biggest gripes.
My top 3 requests at the moment to increase my replayability of the game are:
1. (relates to your point #24, though I think you have a typo saying #25!) Indians give you presents every 5 turns (approx) but have no demands. I want to see one in every 3 of these visits where he needs something from you. Lets say the Incans have run out of food, so that native that has been coming to your village with gifts now comes and asks for 50% of your food store. If you give it to them, he then presents you with the 16 sugar or whatever else you were normally going to get. If the demands are not met they will "not forget this", and your relations suffer a penalty. This has an added bonus in that you might have to think twice about that 'just buy as many guns and horses as you can to sell to the indians' strategy that everyone seems to value).
2. (relates your your point #1) Im with you on the horses, but I do think that horses in the warehouse might not be able to reproduce. I want to see the Stables building generate +1 horses per turn automatically, with the Ranch producing +2 horses, preferably without any food penalty.
3. Finally I think the Founding Fathers are a rush-job and ill thought out. There seems to be no correlation with history for the related bonuses, and many of them are frankly a waste of the political points you have to spend to get them (ineveitably then the AI ends up with these poorer ones). I want to see them redesigned with a view to their personal history, and also to add some balance, strategy, and usefulness to the weaker ones.
again, props for the effort in the original post