I suggest the game should show the price increment for each upgrade. This allows for better planning of prestige upgrades and gem upgrades.
For the gem mechanism, I think it should be immediately useful when unlocked. The game can give player some gems on unlocking it, and also give gems as achievement rewards. These should only give red and purple (and maybe green) but never blue gems.
I think 150 red gems at start should be enough, it allows the player to choose one of the upgrades.