While I appreciate the work you put into this, the simple fact is: the fundamental boff skill implementation (outside of freely swapping skills once they are available) is basically the same as before with an extra layer of complexity and expense. Is balance really going to be destroyed if Boff skill slots could all be III after progression?
The strength of the new boff system isn't that some abilities have a third level now, it's that boffs can learn all of the powers at once and switch between them anywhere.
Say you have one special boff, for example the hierarchy science boff from the delta missions. That 1.5% damage space trait is very nice, but you have a lot of ships. Before, you could only use the boff on ships with the exact same sci skills in their build. Now, you can use that boff on every ship, and switch the skills to keep your build without going to ESD to retrain, and have that pirate trait on every ship you fly.
I understand the hot-swap and that's neat, but it's still the lateral shuffling of the skills that's disappointing. I'm a Tac, so it's pretty much "you can have High Yield Torp III but but now everything else is I".
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Say you have one special boff, for example the hierarchy science boff from the delta missions. That 1.5% damage space trait is very nice, but you have a lot of ships. Before, you could only use the boff on ships with the exact same sci skills in their build. Now, you can use that boff on every ship, and switch the skills to keep your build without going to ESD to retrain, and have that pirate trait on every ship you fly.