That's because before the internet flanderized him he was the most interesting character study in any FF game. Go back and play the game again keeping in mind that he is a nerdy kid 'playing' rogue mercenary. All of the dialogue is fucking perfect.
Yeah, Cloud is far from my favourite FF character, and I really really hated him until *that*, but he is a pretty interesting character. I don't know about MOST interesting, but Cloud gets more hate than he deserves, precisely due to what he's become lately.
Sephiroth still sucks though uh I mean
As for my list (bearing in mind I've played 1-9 and haven't beaten 9 yet):
Minwu (FF2): It's probably mostly because he's the only good fourth party member in the game other than Leon (maybe Josef), but he's one of the best examples out there of a character whose badass character shines through the nearly nonexistent character depiction in NES games, despite only being around until the first boss. (Another good one is Julius from Final Fantasy Adventure.)
Four old men (FF3): Yes, I'm serious. I don't think I've ever seen a "Mr. Satan archetype" (sorry, couldn't find a better name for it) done so brilliantly. Never mind x4.
Kain (FF4): Yeah I said it. Do I need to explain it? Badass armour (I always felt like Kain's sprite looked like an "upgrade" of DK Cecil's sprite), badass Jump animation, and struggles with mind control and coveting his best friend's girlfriend.
Rydia (FF4): One of the most developed characters in FF. She's tempted by the lazy path more times than Harry Potter, lol... She could have wallowed in the misery of her whole village being killed, she could simply have not cast Fire, she could have stayed in the Eidolon village, and considering she spent her growth-burst years with talking animals, she could have just fallen for the advances of the first guy to hit on her. If that's not a strong female character then I don't know what is.
Exdeath (FF5): The most badass villain imo, probably *because* he's sort of a parody villain more than anything. Every time he enters a scene, you know shit is about to go down. Clean and simple. Plus, his castle's made of the corpses of people who pissed him off.
Locke and Shadow (FF6): Pretty much what Jabba said. I especially like Shadow's subtle characterization, and Locke was developed very well.
Terra (FF6): I mention her largely because of how underrated she is. People sometimes blame her for starting an "emo protagonist" trend (though actually to describe any of Terra/Cloud/Squall as "emo" is a gross oversimplification). I suspect that such people are the same people who call Shinji (Eva) a pussy. K, how about you try being used and regarded as a tool, a superweapon, your whole life (and being mind-controlled for at least some of it, though only a dubious Ultimania backstory indicates anything along the lines of how long). This culminates in Terra finally being free in the end, free of even her Esper aspect that shaped her entire life. There's more to Terra letting her hair blow in the wind in the end than people seem to appreciate.
There are way too many great NPCs in FF6 to name, too. If you really think about it, Ultros and Kefka are just the tip of the iceberg here.
Cloud (FF7): Wait, I already talked about him.
Squall (FF8): WAIT DON'T SHOOT ME YET! OK, I get that FF8 crashed and burned on Discs 3 and 4, including Squall's character. People seem to concentrate too long on how the character Squall came to be, rather than Squall's actual character. Being that focused, level-headed, and reasonable is quite an accomplishment, and it makes him a very positive force around others. When others struggle with the idea of violence to prevent violence, or the idea of killing people they don't care about because they're "evil" and/or because someone is paying them to do it, Squall already has all that figured out. It's Rinoa that throws him off. (Too bad Rinoa's such a bad character...)
Zidane (FF9): Very similar to Locke from what I've played. Just a simple, genuinely nice guy who cares about his friends. Also doesn't go overboard with the womanizing.
Vivi (FF9): For one of the laziest-looking designs ever (hey, let's just make Black Mage 3D!!!) he's quite something. I'd probably have more to say if I'd beaten the game, but both he and Zidane have been great characters so far.