The current upgrade system is a huge flaw in the game design, forcing pointless grinding, making unupgraded cards obsolete in PVP events (unless specified as an unupped event), and completely changing the balance of cost/reward. By adding upgraded cards, suddenly instead of grinding for the electrum, people stop giving a crap and grind only for the card, which is worth maybe 20x more. But to be able to grind upgraded cards, you first have to upgrade your deck, slowly, and one card at a time, with the 20x AI3. This splits the skill level of an elements player into two groups: upgraded, and unupgraded, which the other difficulty levels get ignored.
By adding a second upgrade level, you simply create another such gap, forcing more grinding, making new players simply unable to compete because the cards are literally stacked against them, and you potentially risk breaking the game further adding further bonus to certain cards. (Antimatter for cheaper?! Fractal buffed?! A 0|7 Otyugh?! Earthquake costing 1?! S.Nova giving 3 quanta per element?! And god forbid dark matter got his hands on a better version of black hole. )