Since most of the map is already covered by cities with minimum overlap, I am reluctant to add more. I think that in the long run more cities in Europe would make things worse rather than better. It is true that France is a little underpowered, but you have to remember that Germany actually represents all the German states, including the Austrian Holy Roman Empire (extending down to northern Italy), and they got Denmark as a bonus (since Scandinavia is somewhat overpowered). Spain, which was incomparably more powerful than France at the time, only has two Iberian cities, and one in southern Italy that was under their control. This is a general problem with Kal-El's map. Europe is too small to fit everything.
When it comes to Persia, you are right. They should probably be Mongol. However, I want the Mongol, as well as Arab) Empires to be in decline (this is one of the main things that needs to be tested). It may thus be required to reduce their power even further. And I didn't want to just give Persia and Afghanistan to India...
The reason for the emptiness in western US that I want to have the Americans colonizing the west. While this wasn't empty, there were no cities there. The other option, to put the Americans in a locked war with, say, the Siux, to ensure that they expand in the right direction, seems less appealing.
In south-east Asia one could add a civ as you suggest. The reason I left it empty was that I wanted to discourage India and China from expanding to the north. While this was a valid point in the earlier scenarios, however, in 1500 AD it may not be. But let's first see what everyone does as things are now, and then perhaps we can add another civ!