You prefering it doesn't make it "objectively better".
It's not about preference, it's about facts.
One limits you to a set number of skills, which you need to unlearn and learn/re-learn, in order to use more.
The other only limits which ones are available to you within a single encounter.
It is literally as simple as increasing the number of skills allowed in a 'deck' to make the second one clearly superior.
Which is a change in tuning/balance, not a change in how the system works.
A fun experience always trumps the notion of having rigid and inflexible, but "fair" mechanics against AI at every given time.
As established, the rigidity of the current system is a function of tuning, not the fundamental rules it operates on.
Regardless of that: Enemy balance is not set in stone.
They can be made weaker or stronger to compensate for the amount of power a player is able to exert.
AI Enemies can be tuned to a power level that makes it 'fun' to fight them from a position of superior power, with the same abilities that are balanced in a PvP scenario.
That fact makes it(I will use that word again) OBJECTIVELY(based on fact, not opinion), a better approach to balance a game with a PvP component, around that component, and fine-tune the rest from there, rather than the other way around.