I've just started playing this game with my 5-year-old. He loves it, but it's a bit too long for his attention span, so I've thought of the following way to make the 2p game shorter:
* 2x4 huts instead of 2x7 * remove the 5 beige cards with bonusses for huts * remove both green cards of a symbol of your choice * give each player two different symbol cards to begin with (so 4 different symbols to be divided among the two players)
So the starting deck is effectively 25 cards instead of 36.
I've found this to give a satisfying game of just the right length for my son.
Decreasing the pile of huts is a great way to reduce game size.
You could also try putting some resources apart to make setup somewhat smoother/faster. After a few two player games you can get an indication of how much resources you roughly use, the rest can simply be put away for times you'll play with more players.