How about whenever you gain a card you may gain it to either deck? That might make things interesting. (Though you'd need to come up with a precise wording in order to cope with when-gain triggers.)
Also, would the winner be the player with the highest single score, the highest combined score, or would you amalgamate a player's two decks before scoring?
Would a 1 player as 2 player game work?
I've done it with various games. I'll admit to playing Canal Mania 1 player as 5 players, because no-one else wants to play. Sometimes I win.
I mean, it works in the sense that you can play through the moves, maybe in order to analyse potential strategies, but it is a less social experience and lacks that competitive edge.