I actually do like how the game works now, but removing the cap on the upgrades would be nice, but of course that would get a little op so i would personaly add enemy scaling based on your stats, with enemies getting stronger based on what you upgrade. (enemies do more damage the more health you got, enemies having more health the more damage you deal, ect ect.)
it would also be cool if bosses after defeating them for the first time also get difficulty scaling to make sure they arent a joke the second/third time through.