Hey! I'm also developing a game with some Advance Wars inspiration. I also had a UI challenge when developing the interaction with tiles that have a unit + a city. Instead of displaying a window to select the desired entity, I opted to displaying the controls for both. The city controls can be displayed in a small window in a corner and the mouse still controls the unit. I'm not sure if that's the better interaction, but it's what results in fewer clicks.
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Hey! I'm also developing a game with some Advance Wars inspiration. I also had a UI challenge when developing the interaction with tiles that have a unit + a city. Instead of displaying a window to select the desired entity, I opted to displaying the controls for both. The city controls can be displayed in a small window in a corner and the mouse still controls the unit. I'm not sure if that's the better interaction, but it's what results in fewer clicks.