I get that the rules are pretty much a direct translation of the boardgame rules, but I feel that a streamlined rule set for online games, which simplifies some game aspects, could be a good thing for play.
a) You have said that you are thinking of having an option to disable reinforcements for quicker games. There could be a higher number of starting points to buy units with to compensate, so more units at the beginning of the game.
b) Alternatively, one could keep reinforcements but make them less influential. For example, by making buildings the only tiles that generate reinforcement revenue and reduce that revenue to 1 per turn. It would mean holding resources had some importance but would be less central to the gameplay - one would have to hold a building hex for three turns to gain one infantry. Also, reduce the number of turns receiving reinforcements from the current 15 turns.
c) Simplifying buildings. There are twelve different types of building hexes in the game, each with their own defence and attack modifiers for infantry, armour and artillery. Furthermore, to find out what each of them does one has to bring up the terrain table and locate them on it. This could be simplified a great deal by having less different building stats. For example, do a factory, power plant, mine, nuclear plant and oil refinery all need different stats?
d) In fog-of-war, have the map revealed to each side at the start (but not troop positions) so one doesn't have to explore the map to know its terrain.
e) Reduce the stacking limit to three rather than six. Military formations from platoons to corps tend to be organised with an average of three units per formation and it would probably be better balanced in game terms.
f) There are also a few rules I don't agree with, such as negative combat modifiers for being located on road/rail hexes. I see your intention, but I don't think it works well practically. For example, if you're fighting across a road, a negative modifier makes no sense.