I started looking back over what I've done with hacking up SWN to better fit what I want out of a sci-fi system. I'm thinking of switching gears to make the "house system" more in line with Alternity. I'm thinking of using the Broad/Specialized skill structure and cost per skill level as Alternity as well as the level benefits. This also means that character creation would likely end up being more point-based and may also see the inclusion of Perks and Disadvantages. Since the underlying system will still use SWN/OSR mechanics (although I use Ascending AC), I'll still need to work out some of the finer details, but I fully expect to keep things like Cybernetics and mutations pretty much as they are lined out in SWN and Other Dust.
One other change I'm considering is applying Alternity's Low Impact/High Impact/Energy damage resistance models. That means that a character's agility would be the primary thing keeping them from getting hurt with armor lessening damage. I've always liked that idea better than armor making a character harder to hit, but I've typically balked at using armor that way since it's more bookkeeping. It's something that I'm batting around and may likely change back as I test the changes.
I don't know that I'll ever be truly happy with the house system or find a system that fills most of my want list from a sci-fi system, but I hope to get the character creation and monster creation systems down in the near future so I can start in on statting out species and creatures and get down to the really fun part of world building for me, which is fleshing out the galaxy and overall setting details.