Sutsuj, I think you see this all from the perspective of a multiplayer game, where many of the problems that strike the AI, can be corrected by the human player, but are staying big problems for the AI civs. I see these problems from the perspective of a single player game, where the problems of the AI must be taken into consideration. So some features of the Flintlock mod may be working in multiplayer games, too, until now the Flintlock mod is a single player mod.
If such stack limits should be so nice, why are you not using the simplest solution for multiplayer games to set a limit for units in a stack between the human players ? If you play your multiplayer games with a mixture of human and AI players, you should not completely ignore the big problems the AI has with such limitations in C3C. The existing traffic problems for the AI triggered by such tile limitations were already posted above. The argument to make the maps much bigger doesn´t solve this problem, at least if you want still to have an interesting playable map for your game....