We play 2 player using three decks regularly. It works great and we feel it offers more options. With two decks it is easy to get hung on blueprints if you don't get a shot at the cards you need. The blueprints that have only one or two cards are not as critical. We also found it is not as easy to "know" what the other player is planning by eliminating what you have and knowing what's left in the deck.
It plays fine either way. Give it a try, can't hurt to try.
I will! I definitely found that it almost feels like 2p needs an exception of having 3 decks, not 2.