The three-faction situation is directly related to their PvP designs. As far as I know, the players are being kept out of the politics and dealings of the alliances they choose not to join; therefore, having an Enantiomorphic event requiring all three factions would be very hard to pull off. Again, that's a guess on my part, but it seems logical to me.
Also, yes, as others have pointed out, there has been a huge increase in interest in the Enantiomorph lately, and a lot of it does not appear to be legitimate. I agree with Toesock that at least some of it is deliberate on the devs' part: They've discovered that we, the fans, get really, really excited when three people try to kill each other at once. Whether or not they have any lore ideas revolving around these "pseudo-Enantiomorphs," on the other hand, is another question, and hopefully the answer is "no." I also agree, however, that once the fans found some of these Enantiomorphs that appear to be more deliberate, they started seeing them everywhere--which, as far as I'm concerned, is probably a mistake, as it encourages the devs to throw another boatload into the next game.
And since Moon Matrix is absolutely right, if the devs aren't responsible for this mess, they'll have to be pretty damn inventive in order to avoid it in future, if they choose to do so.