Well there is no a "Best" for the whole series, but there is one or two for every game.
FF1 : none ofcourse

FF2 : Leon was kinda ok, but nothing spectacular.
FF3 : None ofcourse.
FF4 : Kain was the one who really got the best design, and the ending left an opened door for his fate. (My fav FF4 character though is Edge)
FF5 : Gilgamesh.
FF6 : That was hard, but I think Setzer had a one of a million spirit really

. Shadow is a close second (While I really wonder why would he leave Relm without telling her the truth)
FF7 : Sephiroth, Cloud or Vincent. Ok I think it was Cloud since Square really made effort of showing how a very normal person with no special talents can be the hero of the game.
FF8 : I couldn't just find a design in FF8 that I can wonder how much time was consumed in giving him all this background. But after some thinking I couldn'tthink of FF8 without Seifer (Anyway he cut Odin to two pieces

). But that doesn't mean I liked Seifer.
FF9 : Kuja and Garland were two unique designs. But I'll say Kuja is better since Garland's personality kinda resembled Fusoya's in FF4 (with the difference in intentions though) Anyway I think Kuja was mistakenly considered a male, mybe it was a translation error

(j/k

, unfortunatly it was on purpose to make him a gay male

. Why you ask? To compete with the Ape man , /looks at the hero)
FF10 : Auron no doubt. One of the best ever designs in FF world.
So what's the best of them all in terms of design? It'll be either Auron or Sephiroth.