I don't know about Sylux's exact identity, but personally I like to think he used to be a top scientist/engineer for the Federation before he started to catch wind of the corruption growing within, and decided to vanish and go rogue (but not before stealing some of their tech). He has legitimate reasons to work against the Federation, and if Samus keeps fighting their battles for them then he'll do whatever it takes to stop her too. My hope is that we can see more of what Sylux is capable of as an antagonist in Prime 4 since none of the hunters really did much in MPH, but ultimately I'd actually really love to see him come back in Metroid 5 (as in post-Fusion, not Prime 5) as an ally of sorts, even if he and Samus operate alone. That's not to say they would be buddy-buddy, quite the opposite actually, but now they face a common threat in the Galactic Federation, which has become completely overtaken with corruption and much more hostile. Not only could Sylux introduce some new gameplay mechanics, but it would be interesting to see Samus and Sylux attempting to work together, and see how the Federation tries to turn them against each other. I could talk on and on about everything I'd love to see in Metroid 5 but that's pretty much what I'd like to see them do with Sylux.