You could get more than ninety percent skills before and more than thirty percent now.
34 skills in total (for CN at least, I counted 33 for some other classes) that's from base to 2nd job including passives. You can get 23 skills, again including passives.
Let's do some maths c:. 23/34 x100 = 67.6470588235% of your skills you can get. (Would be 69% using other class route's 33 skills.)
'But that's with passives, who cares about them' you say? Well well. Let's take IP for this one. 34 skills. He has 26 actives. You can get 17 of them. That's 50% usable actives by the end of it. 17 skills is 4 sets of slots and another skill on top. That's plenty skills.
There's no shortage of skills, gameplay can still be very varied. To me, this update favours players who stay without B-slots since they can get closer to maxing 4 skills instead of a B-slotter who can just max one or two maybe and spread across remaining skill points to the others.
Your issues are with the balance update side of this update and not the skill system. Since the only issue with the new system is where you have to choose between two really good skills but that's just how it is and that improves variety of gameplay since you don't see the same people running around with the same skills. It's the skills they choose for their needs.