Love the game!
I would like to ask for the following (Yes, it's a long list, but don't feel pressured):
The ability to deconstruct/destroy buildings (due to misplacement, for my ocd). I also noted that construction tends to be obstructed by units, but the units don't do collision with buildings. Choose one.
Add hotkeys. For example, assigning numbers for buildings, etc. And make clear the current selection. For example, make a ghost of the building follow the cursor, or make a frame around the selected option (any noticeable effect will do). Keep the selection ongoing till the user deselects. It's cumbersome on the mid game and late game, where the only thing left to do is spam buildings.
Make the pyramid 6x6 instead of the current 5x5. All the other buildings are 2x2, the oddness here doesn't make sense (And I hate that storage bin misaligned).
Make a limit to the amount of units, based on buildings. For example, each gatherer can employ up to 3 workers (arbitrary), and something similar with the military. You could even have the houses work for a population limit (you need the manna anyways to build the other buildings). In that case, how about adding temples to gather the manna/favor instead? Yes, manna is written with double 'n'. Funny, isn't it? Also, add statistics on population.
Make workers and towers be targets too (you can make so with everything, but let's start simple). Currently, you can spam towers and be done for it, since they can't be destroyed.
Try optimizing the game. The assumed workflow per tick should be: Iterate and update logic, iterate and update graphics, skipping drawing over whatever not on the screen (you can add a margin for a smoother camera movement).
As I don't know how you update the map, I can't make better suggestions on how to improve upon it. How about making resources semi permanent, and you have to destroy them manually, using manna/favor? Or use the next day screen to update the map (pausing the logic update loop).