I see card upgrading as little more then a lame way of getting people to play more, that contributes nothing to the fun of the game, but putting that aside...
Problem: Card upgrades make it complicated to find someone to play on a reasonably level playing field.
Solution:
A option to downgrade all your cards for a single match. Someone just started and has no upgraded cards, verses someone whos played awhile and has alot? No problem, both of you click the downgrade card buttons and you can play a more even match (new player is still going to have some difficulty of course)
Or, want to play a random PVP match, but without upgraded cards since you only have say, 1? No problem, just select that option and any and all upgrade cards you have will be temporarily downgraded for the match.
Otherwise one might find trouble getting a game sometimes, and it would be unfair to ask players to have two versions of every deck/card. So this would benefit both people who have alot of upgraded cards, and few/none of them.
Problem two: Card upgrading makes exchanging deck save code much more limited.
Solution:
On a similar note, deck save code could substitute a un-upgraded card for a upgraded card if you only have the un-upgraded version and automatically use a upgrade if available, if the code asks for a un-upgraded version. That way someone can post a deck code and more people can use it, no matter what they have for upgraded cards.