The game is very well-done. I've played a couple of times, and before reading the comments I had the same problem when it came to choosing an upgrade. The selections' shortcuts (1,2,3) should be more clear ingame. The solution and exploit I found while playing was left clicking, then I noticed that when a new upgrade was available I could move the selection with A & D, and apply it with Enter. That meant I would either use the mouse and stop attacking, or something walk towards enemies or an undesirable path to select them. I know this will simply be fixed by telling the player on the start of the game the shortcuts, but this comes with my exploit:
I found out I didn't need the pannel to be opened in order to upgrade, neither I needed any kind of time or points requirements. We can upgrade anytime we want. Once the player clicks on the upgrade pannel, they can simply tap Enter and an upgrade will be applied. That means I can spam Enter throught out the entire game and get myself unlimited early upgrades. Of course, the game gets a little laggy and overcrowed with all that effects on top and all enemies spawning at 8+ minutes.
Following that, the game could have some graphics updates, giving some love to the UI. I really liked the concept art for the enemies, they loose some of they power when scaled for the game, but I wouldn't change the style for the game, since it was well received. The thing I would look at is visual clarity, the background could be less bussy and let the other assets stand out. The upgrade effects could be redesigned, they can be really noisy, the more you have. Specially the Cotton Aura, or passive effects that stick with the player.
Good job with the game overall, I would gladly keep an eye on the game's updates and leave more feedback ♥