As a fairly hardcore KH fan, I have some opinions on this but some of you might not like them. I think Aqua, Riku, Sora, and Master Xehanort are great characters and get the right amount of hype. Here's what I think.
Namine: I feel people are too easy on her (in universe and out). We're told she's kind-hearted and she acts shy. However everyone forgets that she did as much damage to Sora (screwing up his memory to the point of a 1 year coma) as Xehanort and his Dark Seekers put together. There's also her mistreatment of Riku Replica (she treated him at least as bad as the first Organization 13 did Xion). Everyone forgives her because she apolegizes and eventually fixes Sora's memories. Larxene put it too lightly. She's pathetic but has a pretty theme.
Saix/Isa: Despite not having his own boss theme, I think his boss fights are always cool. His characterization however falls pretty flat. As Isa, he's just Lea's edgy childhood friend. As Saix, he's basically Xemnas' lapdog. It's interesting that he contrasts his cold demeanor with a bereserker fighting style but overall he's lacking in depth. Doesn't help that his redemption and revival as a Somebody were rather forced. \
Lea: Axel was a beloved antihero. I feel Lea, his Somebody, doesn't live up to the orignal. Everything about him, from his wisecracks to his powers, seems very watered down. Despite wielding a keyblade, he also feels a lot weaker than he was as Axel.
Kairi's Grandmother: She appeared to spout exposition (that didn't make sense for a long time) in one scene in KH1. For some reason, fans still speculate about her and await her return. There's even a theory that she's a grown up version of Vor (Dark Roads). I doubt she's ever coming back nor will amount to anything other than vague exposition
Sora's Mom: Another character from KH1 who appeared in 1 scene but fans won't forget. She had a single line of dialogue and wasn't even on screen. I don't think there's a mystery to solve here, she just means that Sora has a mother.
Terra: Like a lot of people have pointed out, Terra gets way too much flake from fans. His story in BBS is very good (even if he's a little too trusting of some of the villains) and his gameplay was fun. He also does a great job serving as the muscle of the KH heroes. His character themes are badass. Also Terranort is a cool villain.
Xion: Like Terra, she gets a lot of unnecessary criticism from fans. I feel she's a very tragic character (perhaps more so than Aqua, Ventus, and even Roxas). I know a lot of people didn't care for 358/2 Days but I enjoyed that game for what it was. It helps that both her character theme and boss theme are simply gorgeous. However I feel she shouldn't have been the 13th Darkness (they could've used the empty replica to revive her)
Pete: I feel he's a very effective comic relief villain and a versatile Disney Villain (also the first one). His antics are amusing and his fight in the Timeless River was fun. For all its faults, Re:Coded did prove that he can be a threat on occasion. He also had a moment of competence when he summoned the Illuminator to help Barbossa. Finally I really think his Captain Dark costume was great and should return.
Vexen: He's an interesting character who I feel is very underutilized. I like his ice powers, cloning technology, and his role as a mad scientist. I consider it a mistake that he got benched from the Real Organization 13. In fact, I made a Dark Ambient tribute to him.
I know I may have made a couple people upset but these are just my opinions. Here's my Vexen Tribute.