I love the new skill tree and, to me, it is the best iteration we've had. However, after playing with this version over I don't know how many runs, I would propose a slight tweak on the early skills and one slight tweak for Combat.
All Piloted Ship skills are Tier 1* (*this obviously doesn't apply to the T5 Combat skills but more on that later)
I now believe that all four Technology and Industry piloted-ship skills should be available at any time. It's not that the Tier 1 skills in Tech or Industry (as current) are bad but for certain builds, I desperately wish to skip them. My suggestion is to combine the Tier 2 combat skills into the Tier 1 level and simply require the (current) Tier 3 skills require 2 lower tier skills. (That is to say Navigation/Sensors/Gunnery Implants/EWP and Bulk Transport/Salvaging/Field Repairs/Ordnance Expertise/Polarized Armor would all be T1).
I also don't think the Tier 2 Combat skills are any better or worse than the T1 skills from Combat: they're just locked behind an additional pick. Yes, it homogenizes the trees a bit but having access to the combat skills at any given point gives the player a bit more freedom to boost their flagship.
The first T5 Combat pick is available after 3 points spent on lower tier skills. The 2nd after 4.
That is to say, you can pick System Expertise or Missile Spec after 3 picks in Combat but if you want both, you have to go back down into T1 before getting it unlocked (the 1st T5 skill doesn't count). This just makes the 1st T5 pick one skill point sooner. I'm of the opinion that the T5 Combat picks are not as game-changing as the other 3 trees' T5s, though still very good. I think the first one could be had earlier, though having both should require the full investment.
Partially due to conditions of Suggestion 1, even if I have 5 flagship skills (from 3 trees), I still can't get the Combat T5 skills and I tend to lag behind my subordinate officers. This would lead to more builds potentially having 3 T5 skills from 3 different trees, which is kind of strong, I admit. However, I'm a big proponent of giving flagship skills the most opportunity of all the skills out there because they're competing against hugely influential fleet skills.
Either one would make me happy and save me a skill point or two. I don't like increasing the Level Cap and would like to play as the game is intended but now that I've played a bit, it would help my playstyle a lot to have these tweaks. You may disagree!