Just doing the main series (no spinoffs or sequesl) I would say FFVI is the best in the series. I don't believe it's perfect but it's few flaws are so minor to me when compared to the good qualities that it just seems stupid to be nitpicky.

FFVI, for me has quite possibly the best cast ever assembled in an RPG. I honestly don't hate anyone and that's good for me. I usually hate 50 to 90% of most RPG casts nowadays. Except for Umaro and Gogo (I consider them "secret" characters anyway ) I feel every character really brings something to the story. The fact that the game has such powerful scenes in it without having to resort to anything "flashy" shows how powerful the characters and story really were. Previous FF's have moments as well but not the sheer volume that FFVI has. The game really is an opera...

As for the characters becoming "clones" it really started in FFV and like any game with the "clone" problem. I feel it falls down to the players choice. Yes the option is there but you don't have to do it. Hell, I barely teach magic to half of my party. I aslo feel most of the characters have enough distinctions between them, thanks to their job class abilities, that making them clones is impossible unless you resort to using magic alone.

The game is a little too easy for my taste but most people act like it's FFVIII bad when it really isn't. Maybe by end-game but what post-FFIV FF isn't ridiculously easy by end game?

Now I really don't understand what the hang up with the WoR is. I really don't feel like anything else needed to be said after the world was destroyed. and I thank god the game doesn't place you on a smurfing "rail" on how to do everything. I like "freedom" in my games. I also love when my games act like games and not interactive movies (Looks menacingly at FFX ). So the abilitry to "choose" how to go about the story is a plus for me. I feel the WoR is more about the characters finding closure storywise.