Just a few quick ideas from other RTS games and Ages games would be:
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Easy military drag. Eg. villagers aren’t selected when you do a wide box over an area and only military units will be selected.
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Automatic gathering. As in, build a storehouse and units gather automatically as they do in other AoE games.
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A select all army and a select all navy hotkey. Just easier than scanning the mini-map for scattered units and convenient in general. If the ctrl groups can’t be that large perhaps just a rally point for all units.
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Smart unit queuing. E.g. If I select 3 barracks and queue 3 axemen, each barracks will produce one, not queue them all in a single barracks.
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Mini-map indicators for attacks and a hotkey to cycle through the latest alerts.