I guess I tend to judge the protag in how well they fit within their cast too.
Best:
Cloud is completely iconic. His design actually means something and is consistent within the lore and world of VII. The whole cast is more or less 'working class' design, and I appreciate how that fits within their world.
I love the look of XIII's cast. Lightning, Fang, and Vanille have top-tier female design for me (coming from a woman), and Sazh and Snow aren't bad either. Hope falls a little flat but his aged version in XIII-2 makes up for it.
Nomura's version of Firion. Spot on homage to Amano's design that translates beautifully to the world of Dissidia.
Bad:
Much like anything related to Squall, I just don't see how his design is 'good'. It looks like bad 80s to me (the whole cast is drab and uninteresting, barring Edea).
As much as I love X, Tidus looks like an idiot. And Lulu is SO close to fitting a black mage character, but misses it due to the belts and impractical neckline. And don't get me started on the designs of X-2.
Much of the cast of XII looks great at first blush, but then you start to notice the nonsense. Yes, Baltheir and Fran are great, but Vaan, Ashe, and even Basch look super silly in the details.