While I can play with very big maps in vanilla, I should not do this with my mod. It's just way to slow in later eras.

Does anybody know what is causing longer round times in mods?

Mod Comps in my mod: BUG Mod, Better BTS AI and tons of new unit classes, leaders, ...

Better AI becomes more computer resource demanding in later eras, as there is more logic to run through for all the units. Also the poly counts of the models for your custom units start to make a huge difference, this is why I've limited the models to 2000 polys in LoR. Finally the BUG PLE (plot list enhancement) code is pretty unwieldy and can cause slowdown if there are large stacks present for the human player. So the best way to improve performance for your mod would be to sack all the high poly models you are using, and disable the PLE in the BUG options.