A few comments:
1) The Settler Map is way off. I like the new size of the map, however. It's not as unnecessarily large as the other map was, and the palm forests are also a nice touch.
2) Because the Settler Map is so off, I am forced to use the world builder to change the name of the towns myself, and then, for some reason, my game inevitably crashes. It's annoying, but I am still waiting to see if there is any solution to it.
3) The new merc system is a really good idea, and the stylization of the mod as a whole is really starting to come together. That being said, I think that the graphics of the galleys and early war ships of the civs could be customized to look differently. At the current moment, the Arabic galley looks entirely similar to the Venetian galley.
4) The biggest errors to the Settler Map has been in Iberia. al-Garnata (Granada) was near Madrid, and that's obviously not even close to the reality of the situation.
5) I like the new colonies screen. It's another stylistic touch that gives a nice "RFC Europe" feel to the mod.
That's about all the comments I can think of for now, but I am sure that there are other ones floating around in my mind.