This has been really interesting. Some thoughts:
1. I never imagined FFX-2 had so many fans, and I'm one of them -- to an extent. I have to agree, though, that the Garment Grid/Dresspheres system is actually quite good if you can manage to abstract it from its cutesy labels and undertones.
2. I thought the Junction system would get a few more votes. I mean, I hate it, and it's obvious many others do, but FFVIII often gets many votes as people's favorite FF game, so I figured there must be more people who thought it was great.
3. I believe those who complain that "after a bunch of grinding, every character ends up being the same" are being unfair. By excessively grinding, I think you abandon any claim to what might reasonably be called the "intended game experience" in favor of something else entirely, even if it is to reach some in-game goal, like defeating superbosses. It's not a perfect analogy, but that's like saying higher education is flawed because, if you spend 50 years in college, you can major in everything. Well, yes, but you're not meant to, and I think that counts for something.
4. Perhaps predictably, it seems like most people's answer to this question comes down to whether they prefer freedom and customization to defined, plot-reinforcing character roles, though there seems to be some consensus about the fact that the best system should somehow allow for both.