My wife and I are both eager to see what FFG will do to fulfill this hint found in the official CE FAQ.

Q: Can CE be played with only 2 players?
A: There is no official 2 player variant for the current edition yet. There are existing 2 player rules for the Eon edition that can be found on the web. We will be releasing official 2 player rules for the current edition as soon as we get a chance.

Will there be 2-player rules in the upcoming Cosmic Incursion?

Well, none of the previews have mentioned it. If there was a 2-Player varient I would think that it would be a big enough deal to be mentioned in the previews.

So we don't know, but it doesn't look good....