I never played Riku's story, but I didn't really enjoy Sora's story. Especially how he started fighting the Riku clone over Namine, being a totally clueless idiot. I know, the Organization did it to him, but still, it was painful to see him acting so dumb. In the end it was all "Namine this Namine that".
Did they really attack Sora? If I recall, Sora attacked them first.
Anyway, they are a bad guy organization, and everyone loves bad guy organizations. Just look at Akatsuki in Naruto or the Espada in Bleach. They're also a refreshing change from everyone and their mom who wield Keyblades.
That's game-mechanic wise, but why did they show up story wise? I personally think they just wanted to scoop Sora up, and the one who stayed behind (don't remember who it was) especially wanted to mind**** him. Sora had no idea what he was talking about.
I'm not a big fan of the Final Fantasy series, I've never played FFVIII and I only played FFVII for halfway through or something, but I like Leon and Cloud, although a bit more action would be nice. Especially in KHII Leon was a bit dull, restoration comittee give me a break. It would be nice if you could add Leon or Cloud in your party or something.
Also, it would be awesome if they could add Vincent.
I don't think KH should distance itself from Final Fantasy to get its own image, because Kingdom Hearts revolves almost entirely around Disney worlds, and some of the most important characters are Disney characters. Kingdom Hearts will never completely have an original image, it's just a mix of Disney, Final Fantasy, and original characters, and it works.
I'm already doing that but that just gives you a lot of HP. I can take maybe three hits from Sephiroth without my health bar depleting and then it starts to go down