It's a fanboy thing to say, but I love the series overall. Some aren't perfect, and others tried new things that just didn't work out so well (FF2's leveling system, FFVIII's draw system).
I think the worst is FF1. Not the NES version, not the GBA version, but the PSP version. It's embarrassing that SE wanted to sell you a prettified version of that game for $30. They added some nice stuff, but the core gameplay is the same (that is to say it's 20 years old). Had they bundled the remakes of 1 and 2 on the same UMD, it wouldn't be a problem. By itself, though, the PSP FF1 is a travesty. Strangely enough, the steep entree into FF2 (getting over the leveling frustration enough to get into the game and enjoy it) disappeared in the PSP version, and was my favorite revision by far.
I'd also throw up the DS remake of FFIII. Having played through the NES version, I simply prefer that as a piece of nostalgia. The slapped-on story was paper thin and did nothing for me, and the extras didn't really do it for me either.
I'm of the opinion that not all FF games are equal even when talking about different versions of the same title.
FFIX's story almost completely escapes me. I remember enjoying the game, but I can't recall moments from it the way I do the others. So for that, by default, makes it the "worst." But I'd still gladly play through it again.
Here's a question I'd like to see opinions on: what's the worst FF minigame? Blitzball, triple triad, the card game from FFIX? Something else? Chocobo races or the entire golden saucer area?