If Vancian magic is really just a disguised spell-point system, does that mean there's no reason to favor one over the other?
No. It's just not about mechanics.
The reason why non-Vancian proponents object to Vancian magic is not because they don't like the math, but because they don't like the model. Vancian magic assumes that magic is mostly about the preparation: call it "memorization", or don't call it that, but in a sense, it's not about who the spell caster is, but what the spell caster has done. It's possibly to describe a Vancian spell as being powered by purely natural forces surrounding the caster, rather than power inherent in the caster.
Non-Vancian spell point systems, on the other hand, usually model the spell caster as a battery that stores magical energy. You expend power to cast spells; when you run out of power, you must recharge.
For some people, that's a preferred way of imagining magic, so they dislike the memorization model. On the other hand, I dislike the magic battery model. So, of course, I prefer Vancian magic. Or rather, Vancian plus some other systems, which I'll talk about in a future post.
This is the only real distinction between magic systems: which one matches the way you imagine magic working?