Actually I have similar problems with small map, 3 factions, turn 20.
Custom race on custom map (map editor, start from empty map, nothing spectacular, balanced for 3 players).
I have only 8GB ram, so it is swapping heavily.
other specs: core i7 with hyperthreading enabled, Windows 10 x64.
I encountered this with both 3.02 and 3.03 (I did not play with earlier version recently).