I think it(lag) has something to do with the number of types of units too,I remember reading that with Rhys scenario that that was an advantage of plague... as the game progressed all the older units warriors archers etc were removed from the game and the later plagues removed all the middle group of units... and i never had any problems with it, so it sounds feasible
My last game (GEM) I started on the best settings and progressively lowered the specs as the game progressed, till I won it, late game saved when it black screened and reloaded from desktop every 2-3 turns, (Marathon) but that was with about 40 civs active by the end and you could still come across archers and chariots, its not that bad when I play a standard BTS game and just lowering the specs as the game proceeds seems to do it
thats on my laptop too... a good one... but 2 years old