MAA´s City mod changes different files, so these two mods should be compatible O.K. The only thing that MIGHT cause a trouble is the CAMPAIGN_SCRIPT.TXT. I do not know whether MAA already applied the UnitSize fix...

I would recommend to install my mod first, than the City mod and run the game to see, if UnitSizes are O.K. - from the second turn on, all your generals shoud have a trait saying what UnitSize you are playing on.
If it is not consistent with your actual settings, you would have to download the fix (see the Bug Forum) and copy the relevant part of the fixed CAMPAIGN_SCRIPT.TXT into the MAA´s one.