Double dipping is not useful because the level cap is too low IMO. If the level cap was 20, I would definitely wrap over getting 5 skills in all trees.
Also, the only place where I see piloting specialization being an issue is with phase ships, otherwise you just take shields + armor and are good at flying everything else (except maybe carriers, but who wants to personally pilot a carrier). Those phase ship skills didn't exist at all in the last patch, so those are additional choices. You can still fly other things too, I sometimes fly doom without phase skills, and it's pretty much the same as doom from the last patch, which was good.
I definitely agree that not every choice is as interesting as it could be, and some rebalancing is necessary, but I think it's a lot closer to that goal than the last skill system. Old tree just meant you took all the obvious best skills and then decided which unimportant/QOL skills to give up/take. It was incredibly uninteresting.