MoM can be quite a chore as well when it reaches late-game stages. 90% of the time is spent watching those silly animations that pop up when each city finishes what it is building and choosing a new building/unit for that city.
The solution, of course, is robust build queues that can be named, saved and applied to cities both singly and in groups via a flexible multiple city management screen.
The tedium of micromanagement is really not a game design issue at all, merely a user interface design issue. The creators of MoO3 did not realize this and unfortunately that game is the tragic result.
I guess the other major issue with MoM, for those with optimization-OCD (like my friend) is the problem of waste. All excess production, food and research when the current task completes is wasted. This is quite simple to deal with using a carryover system.