I have played two games with 2 players. All of our games are played 2 player so I was a bit worried when I purchased the game.
The first game we played was according to the 2 player variant in the rule book. It was okay, but I just wasn't satisfied with each of us playing 2 colors. It just felt too clunky or fiddly. I demand smoothness in games and I am probably more picky than most in that regard.
The second game we played we played with no variants at all. We each played one color and we only used 2 ships (which I was worried about initially.) Turns out the game was really fun! There was tension and competition and it didn't feel broken or lacking at all.
I was afraid the game was going to go to the trade pile after that first game, but after the second game, no way! This is going to go down as one of our favorite games. Rated it a 9. I am sure it is better with more than two, but for us it was a really good with just the two of us.
Wow. I really wish Bruno would comment on this. If what you are saying is correct (I believe you) then why add the variant?