First of all, thank you for this very thorough analysis, that means a lot.
Double-clicking on unit for selecting all of them is actually already implemented, but not told through the tutorial and the click check is a bit too picky, I need to refine it. Also, you can manage the sound options through the pause menu (Echap > Options > Sound).
The option to switch between auto attacking towers VS going straight to goal is actually on my "ideas" list, I am glad to see you thought about it too, I will prioritize this. I also like your idea of counterplay in unit/tower behavior. I had some vague idea that I needed to do some kind of synergies but I couldn't figure it out, you brought in fresh ideas I need to consider.
Regarding upgrades, after the 4 unit unlocks there are also some meta upgrades for the units and gameplay. I indeed need a few more upgrades and balancing between their cost and the earning rate to avoid the situation you had. On the "in-game" upgrade points, that is a wording and tutorial issue. You actually gather "experience" during a level by destroying towers, and this allows to get some unit improvements between wave (using the "up" button on the right of the interwave screen). I will work on the UX and tutorial for this so it's more readable.
I will also add the QoL suggestions to my todo list (hotkeys, icons, performance, visual distinction of out of reach towers...), they are very valid points.
Thanks again for playing and for your advices!