The game looked really fantastic! And it was a great idea, I'd add a few invisiblity frames in between upgrading though as I would take some damage but I got surrounded so I kept taking damage, upgrading, taking damage, upgrading.
Also maybe give the player a few seconds to realise the upgrade screen is there, as I was clicking to shoot I sometimes accidentally picked an upgrade (you could add a "confirm upgrade" button)
nice work overall!