Now that I have played the game, I have a few suggestions to making the game better without modding to much. Being a computer analphabet myself, I can not do much, and don't really have the time to learn to mod, anyways, here is my humble suggestion:
In my view, faction colours are normally needless, and they are way to bright and dominating in M2TW, a great improvement from RTW, but still, there is still a bit of lego feeling to the units.
A great thing about this game though are the mercenary units, Turkopoles, Flemish pikemen, Balkan archers, Armenian Lancers Kazwarmian heavy cavalery, Crusader knights etc. They are without faction colours, and look great. My suggestion is therefore to replace the faction units with mercenaries as far as possible, and make the mercenaries buildable in the areas where they can be hired (Flemish in Flanders, Balkans in the Balkans etc). Though I know wery little about modding, and we haven't gotten the pack extractor yet, I suspect this will be easy for people who know this sort of thing.
Also, and this requires skinning, the Order knights look awful, Black Hospitallers on red English horses. The faction horses for Templars, Hospitallers, Santiago and Teutonics need to go, and fast!!!.