I think part of the problem ends up being that 2/2 enemy split is so rare. The thing is. The 2/2 split makes the end boss pacing different, and in my opinion better. The problem is the 2/2 split gives the player too much territory on their plane. Something like a 3/2 enemy split, with 3 ai on the players plane and 2 ai on the other plane would IMO be ideal. So the problem basically just boils down to the fact that 4 is too small a number to divide in that many interesting ways. So, in CoM 2, even without a ton of alternate gamemode variants the default variant could just use alternate fraction for how many ai there are per plane, with say 5 opponents being split 3/2, and well any and all other numbers you can think of adding to the game having various break downs. Possibly with 12 ai enemies the breakdown could be 8/4 or randomized to also include 7/5 and 9/3 and such to keep the games varied.
Another option might be to divorce the land mass size setting from being identical on both planes. Perhaps if you select small landsize it will give arcanus small landsize and myrran tiny landsize (aka one size tier smaller). This would significantly nerf settlers on myyran and maybe even allow you to improve the mineral/treasure quality of myrran back closer to it's original 1994 state (where it was just crazy OP). I agree though most of these problem seem much easier to solve for a potential CoM 2, and CoM 1 might be in an ideal place.
Another option might be to divorce the land mass size setting from being identical on both planes. Perhaps if you select small landsize it will give arcanus small landsize and myrran tiny landsize (aka one size tier smaller). This would significantly nerf settlers on myyran and maybe even allow you to improve the mineral/treasure quality of myrran back closer to it's original 1994 state (where it was just crazy OP). I agree though most of these problem seem much easier to solve for a potential CoM 2, and CoM 1 might be in an ideal place.