I enjoyed the blog, it was an interesting read. I'll try to take the "there are actual numbers in this post please don't make me regret it" to heart and try not to focus *too* much on the magnitudes of values.
At its current power level, Neural link certainly feels better being a non-capstone skill pick, although it does make me a bit sad, since it made sense as a capstone due to its uniqueness. However, as a quick tweak, it is a simple and effective solution. Although I'm going to have to mock up a 72 DP Radiant with 25 more OP and the ability to take BotB at the same time, because that is quite the buff (like an extra 10,000 flux capacity)
Cybernetic Augmentation moving up in its place is starting to feel like the generic boost alternative to BotB now, but more flagship centric. Certainly it feels worth taking Tech to 5 now if you're not planning on using automated ships.
ECM still feels a tad clunky, but should work I think. Having the Electronic Warfare skill actually add an extra side benefit to ECM in general seems the right way to go. Quick captures is an interesting alternative to BotB deployment bonus, and the ability to negate ECM entirely seem good. 40% is doable, and means you don't need to compete with 60+% an Ordo or two can reach.
I do like the decoupling of Hull Restoration's in-combat benefit from Best of the Best, which makes it easier to stand on it's own separate from leadership. Random thought: Given the +10-15% CR is being removed, and some d-mods these days drop max CR, what if the tier 3 industry skills (Containment Procedures, Makeshift Equipment and Industrial Planning) all gave +5% max CR to all ships in your fleet? It would mean industry tree could help counteract a few more of the negatives that some d-mod fleets bring to the table, as well as meaning you could in fact have 100% CR without the leadership tree.
EDIT: Exactly 40% is in malfunction territory. It has to be at least 41% CR to be in the white.
It's yellow but that actual malfunction chance will be zero, IIRC.
If I understand the Hull Restoration proposed numbers correctly, Hull Restoration drops the DP cost of the pristine Radiant by 10% or 5, which ever is smaller. 5 is smaller than 6. So, 60->55. Alpha Core multiplies DP by 4, so 55*4 =220. 120/220 * 100% = 54.54% from Automated ships. 70% base - 100% (automated) +54.54% (automated skill) + 15% (combat endurance) = 39.54%. Is sub-percent CR tracked? I vaguely remember it was but perhaps I'm wrong. So unless the code rounds up, or true threshold is more like 39%, it looks to me Hull Restoration + Combat Endurance would put you in malfunction territory with an Alpha Core Radiant since it is below not quite a half a percent below 40%.
Interestingly, a 54 DP pristine Radiant would be above the 40% threshold at 40.55%, but that would require lifting the 5 DP cap.
As for the various elite skills, I think I tend to agree that just more damage bonuses on the defensive focused skills, while it works, is kind of meh. I do like the idea of moving hull repair back into Damage Control.
In regards to the damage type resistances with the skills, I think the issue with the damage reductions that used to be there was they stacked on top of what they were already good at. More kinetic resistance on hull and more HE resistance on shields. The other way, but smaller bonuses might work (i.e. more kinetic resistance for shields and more HE resistance for armor). Other stats that might make sense for Field Modulation include flux stats, or its manipulation. A +25% vent rate would be a good match for Field Modulation (for both phase and shield ships), but that is already on Polarized Armor.
Impact Mitigation is a bit harder. I'd almost suggest taking a page out of the Damage Control book which reduces damage by half if above 600 once per second, although that really is anti-torpedo which is what is designed to take down armor.
Crazy idea (not necessarily good) might be something that slows down armor stripping, but maybe not hull damage. Limit armor cell damage taken to 50% (or 34% or something) of original maximum from a single hit. So an undamaged Onslaught takes a reaper to its 1750 armor. 4000 HE means 8000 / (8000 + 1750) = 0.82 damage multiplier. Armor would normally absorb 1750/2 = 875 of the 3,280 reduced damage, leaving 2405 to the hull and 0 armor in the armor cells. But Elite effect could be that 875 armor is left in the cells in this case, but same hull damage is dealt. Mostly an anti-torpedo measure meant to prevent complete stripping from a single lucky shot, but probably too niche.