Progress in this game absolutely grinds to a halt after a certain point, and it is long before you should have to be thinking about resetting. The upgrades just aren't substantial enough to keep the game moving.
Why are these games so popular? Terrible writing, entirely derivative and unoriginal gameplay, borderline copyright infringing music, and it was obviously drawn by someone on Deviantart.
The people who are complaining about not being able to max out their skills don't seem to understand that you aren't supposed to be able to max them out...
You're supposed to strategically place them to match your play style.
The kongregate API has most likely glitched. Try refreshing.