When we designed the Portable Galactic Empire, one of the challenges we faced was how many people would be allowed to play out of the box. We went with a maximum of 6. However, I would not say that is the ideal number. Truth be told, they probably aren't enough cards in a single set for six players, with the exception of monuments.
For a two player game there are too many cards. If you wish to play a two player game of PGE, I would recommend reducing some of the cards. Remove 3 or 4 sets of weapons as well as half the defenses. Reduce each of the improvements by a count of 6. Reduce the planets and systems by removing all of the larges. Finally reduce the number of monuments in the deck to 6. Victory now requires only 4 monuments.
Unfortunately, with only 2 people playing the chance of stalemate increases. As a result I also recommend you use a sudden death rule. After a monument has been played by either player, each player rolls a d6 at the start of their turn, before the Invasion step. If the result is a six, the game ends without playing that player's turn. The person with the most monuments in play wins. If there is a tie, use resources as a tie breaker. The person with the largest pile of stuff wins.
We haven't really play tested that enough to know its going to work 100%, but it should make for a faster game with 2 people. As always, you should remember that any game out of the box is a framework how you choose to play it is ultimately up to you. And if you come up with what seems look a cool variation, let us know. We love to hear from you.