Second it required SaGa levels of exploration to find anything of note
No, it didn't. Usually walking into a newly-opened land was enough to start a quest there, and almost every land HAD a quest present in it as soon as it was placed. I think the Pirate Ship and some of the Dragon related-areas didn't. Around five or so just trigger automatically after a while when you go to your home. I mean there were SOME fairly obscure quests (The Nic line, Gilbert line, and the three or so that required domina to have a specific mana level. These amount to maybe 11 quests total. The second quest in the fairy storyline also has odd start requirements. So let's say 12) but not the majority of them.
Dragoon arc was both the easiest to find
What, no. The Jumi arc is the easiest to find. You start it by walking into the pub in domina, which is the third building you see in the entire game. And almost every artifact you get from the quests open up lands that are strictly relevant to the Jumi arc. And a lot of quests start themselves just by going to the relevant area.
First its gameplay was horribly broken
It's Square. What do you expect :( It works a lot better on hard mode, though (especially if you use someone like Larc as a companion, because the AI for the fighter characters is far, far more functional for some reason).
Also I have to note this just because I was playing both recently, but in general the partner AI isn't nearly as bad as I remember. It's maybe on par with SoM, but nowhere near SD3's quality. Only Bud and Pearl are completely and totally useless. Like, Larc is really effective and Lisa manages to hold her own, somehow. Lisa is odd since she SHOULD have the same AI settings as Bud. I think it's because her broom counts as a spear and his pan counts as a 1h axe, which effects attack range. IDK.
SoM's oddity with Sprite behaving like a tard might be because most of the weapons he's good with are ranged, and ranged weapons behave weird and the AI grid isn't really intuitive for them.
Wait what does this have to do with villains.
Here's an interesting thought. Giygas isn't remembered for anything he DID because he didn't do a lot, but rather his vague and incomprehensible creepiness. Giygas was, ultimately, just a twisted face/fetus displayed as a background.
His aesthetic's really important since visually it's hard to discern even what he is. The thing is, square did similar things with some of its bosses, like Zeromus. Except Zeromus... well, it's Gigerish, but it looks like an alien with a severed dong (http://www.ffinsider.net/final-fantasy-4/sprites/boss/Zeromus2.gif
srsly it does). It's WEIRD but it's not incomprehensible.
Giygas was just red and black fractal noise in the shape of a horrified face/baby.
Alternatively, keep watching the What ARe You PLaying? thread for my EVENTUAL let's play/screenshot tour of tong nou, as I attempt to explain why it's creepy and weird.