No, I think the fundamental flaw in the way they did it is because they put the old skills, which are pretty much independent to each other, in the binary choice system instead of making skills that fit the system. This is why some gameplay styles are broken now, not just because of the nerfs.
If they wanted to make you choose which skills to pick, they could do that just with the higher SP cost per skill. Since the skills were already obtainable together, there was no bad chemistry between them to force them to be incompatible with this system.
It's an useless layer of complication that hurts usability, and at best would be redundant because of the SP cost. Right now it's bad because some choices are broken, but even if they find an ideal setup, it'll still be redundant and probably kill off some skills because the other choice is much better.
So they either had to take more time and make a lot more skills to have as alternates, or not have the binary choice at all and just increase the SP cost for maxing out stuff.