Glad to hear you are having fun with the skill. It sounds like a very frenetic way to play the game.

Neural Linked Afflictor-Shade tag teams are insane. Why?
- 700 base flux dissipation, x2 if you run Phase Anchor - almost a Radiant of damage potential!
Given a Radiant can run 2 large missile racks and 4 medium missile racks along with its flux dissipation to run flux consuming weapons such as Plasma Cannons, I don't think comparing raw flux dissipation is going provide a full picture of damage potential. Don't get me wrong, +50% damage on top of 4 AMB is a lot of damage, but the biggest multiplier of an Afflictor's damage output comes from the ability to bypass shields. Which for me would mean Adaptive Phase Coils instead of Phase Anchor for more speed at moderate hard flux.
I'm also curious about the actual loadout. Neural Link + Phase Anchor is 13 OP of hullmods you can't s-mod. I can't seem to get a reasonable Afflictor build with 4 AMB and those hullmods. Are you only running 3 AMB on the Afflictor? I always thought the Afflictor was about burst damage, not DPS, since if you need to make 2 passes instead of 1, it is going to take twice as long given the nature of phase space, hard flux buildup, and slowing down.
I guess I'd want to know how much worse it really is with just an officered Shade ordered to escort your Afflictor instead of Neural link jumping between. The other thing that strikes me as hard to deal with, if you de-phase, the other ship is potentially going to recharge it's AMB in about 1.7 seconds of subjective time (10 seconds/6=1.7) if it is running Phase Anchor, and then take some pot shots. It really does sound like you're jumping between each ship every 5 seconds or even more often.
- Neural Link cooldown resets get you 100% uptime on Entropy Amplifier/EMP when needed.
I feel like when I was piloting an Afflictor, the Entropy Amplifier cooldown didn't feel like it was limiting my DPS that much, although I admittedly had System Expertise and Adaptive Phase Coils. If you're using Phase Anchor, I can see this being useful, but on the other hand, I assume you are cutting into your overall damage potential by 25% by dropping an AMB.
The amount of map control two phase flagships exert is amazing. No gap goes unexploited.
Do you really find that it is much more than a single Afflictor, or an Afflictor with AI Shades/Afflictors along for the ride as Escorts or generally ordered? I'm kind of finding it a bit hard to judge. A single Afflictor flagship already exerts a lot of map control.
I haven't experimented enough with the endgame, but there's fascinating options (Harbinger tag teams! Doom & friend! Infinite* AAF Atlas or Eradicator cheese!) I haven't seen tested.
I find in the case of charged systems, the reset isn't nearly as valuable as on a long cooldown, non-charged system. For short cooldown systems, you're not getting all that much more uptime. So you'll get a lot more benefit to the Harbinger tag team than AAF ships, which already have 50% up time, or a Doom. Systems Expertise is already a much larger multiplier on a Doom than Neural Link would be.
And on the capital variants, like Atlas Mk II, it eats up 25 out 220 OP, more than 10% of it's fitting OP. Plus an Atlas MK II really wants Missile Specialization for its two large missile slots, which Neural Link prevents the bonus missiles on one of them. Same goes for something like an Astral (2 large missile), Legion (5 medium missile), Legion XIV (2 Large missile), Conquest (2 large + 2 medium missile), Executor (2 large missile), Pegasus (4 Large Missile), Invictus (2 Large missile), and Odyssey (1 Large + 3 medium missiles). Even Onslaughts will kind of be sad with their 4 medium missile racks.
Now that I think about it, the only capitals that wouldn't care significantly about the lack of +50% more missiles are the Paragon and Retribution.
I almost went to try out Neural Linked Nova, to see how good it can be in player's hands. Then I remembered, oh right, capital costed Neural hullmod, screw that.
On the Nova, you are trying to work with an a hullmod that is specifically designed to nerf the Radiant in player hands, and the Nova is no Radiant.
50 OP out of 280 OP on a 40 DP ship hurts even more than the 50 OP out of 320 OP on a 60 DP ship.
Neural link certainly enables a different playstyle, but I'm not convinced said play style is actually as strong as other capstones.
There are a lot of opportunity costs associated with the Neural link skill:
1) It uses a capstone skill slot.
2) It prevents combat endurance and/or missile specialization on one of the two ships (which makes it a poor choice for missile ships, and generally is a relative -5% damage, +5% damage taken, -5% speed compared to other ships).
3) It costs OP, and a significant amount on a capital (25).
4) It costs a huge amount of OP (50, 15.6% of a Radiant's budget, 17.8% of a Nova's budget) if you want to combo with Automated ships. It would be like if Derelict Operations + Support Doctrine capital ships had to pay an extra 25 OP to use both skills.
So having paid that price, what do you get?
An extra officer (with said skill omissions) or alternatively viewed as an extra officer and an extra pseudo officer when you transfer out. And on small ships, or far away ships, a significantly faster swap time. However on a pair of close capitals, you are saving about 1-2 sec in transfer time. And potentially a combo with Automated ships which let you fly ships you wouldn't be able to do otherwise, but at a significantly reduced capability.
Consider this potential comparison. Onslaught + support Pegasus escorting it, with Neural Link in one case, and the +2 officer skill Leadership as the alternative skill pick.
Neural Link Case:
5 second swap time at escort distance or far away
85% CR and no extra missiles on one ship
-25 OP for each ship
FMR and Burn Drive extra Resets
Full player skills to both ships other than Combat Endurance and Missile Specialization
Officer Management Case:
Start the battle with the extra two officers in the Onslaught and Pegasus.
Use X to transfer into one of them after battle start.
6 second swap at escort distance, about 25 seconds half a map away - however you can enforce escort distance by commands
Don't need to take Missile Specialization or Combat Endurance on the main character, still get 100% CR and extra missile for both ships.
Only benefit from player skills when fully in one ship, other ship gets base officer skills.
In the case where I'm doing close coordination between the two ships, i.e. escort distance, both ships are significantly stronger in the Officer Management case than in the Neural Link case, unless I'm running a very heavy combat skill build.
I realize the combat endurance and missile specialization issues are quirks of the system, and not ideal interactions, but the fact of the matter is they are there. It seems not great from a design perspective that I can get better tag team performance in some, admittedly corner, cases explicitly without the Neural link skill than I can get with it.
The case described here, multiple phase ships, is probably a best case use of neural link, with utility falling off strongly in the capital cases, unless the capital has a long cooldown non-charged system - like say the Astral.