The blog was an interesting read and I like the direction you're taking things.
The argument about "game changer" combat skills locking you into a limited ship style makes sense, and I can see why you didn't want to go that route. And I can't deny that in skilled hands the power of current combat skills are a significant force multiplier.
Although, to be honest, Neural link almost sounds like a "game changer" combat tree skill hiding in the technology tree. It certainly gives you a good reason to spend points in the combat tree. Not that I'm complaining about the location. Putting it opposite the Automated ships sounds about right. I expect to see Monitor + Radiant solo player fleets.
I like how there's some clear mixing and matching to be done. Assuming we are still limited to 15 skill points, and just the top abilities, the combinations look fairly varied. So we've got the combat tree in general, best of the best, support doctrine, neural link, automated ships, hull restoration and derelict operations.
Keeping in mind that neural link gives you the most benefit when combined with combat, and hull restoration and derelict operations don't mix, you've got something like 14 reasonably distinct combinations that look like they should play differently. Sounds pretty good to me.
Although I do have a few questions. Given we now have percentage reductions in deployment points for ships, will they be allowed to be fractional, or will they be rounded? For example, does a Lasher without officer and under Support Doctrine cost 3 DP, 3.2 DP or 4 DP to deploy? And does Support Doctrine add with or multiply with the reduction from Derelict operations (20+30=50% off DP costs?). That will allow for some interesting fighter saturation attempts. Assuming they add, and if you get choosy with your D-mods, you can get something like 18 Herons worth of fully operational fighters in 180 DP (or 36?! Condors).