Story-wise:
BbS=KH > Re:CoM/CoM >>>>>>>>>>>>>> KH2
I'm sorry fans of <insert character I hate>, but I hate Roxas, I hate Xemnas, I hate OrgXIII, and I hate DiZ, I hate all the garbage that was in KH2 and then bled into 358 Days. I'm not rating Days because I could not stomach playing through it, the gameplay is garbage, the camera is garbage, the graphics are pretty bad and it's a total recyclethon without having an interesting battle system. The panel system is great, but it's meaningless when everything sucks. Also, Roxas sucks.
Birth by Sleep returns to the more traditional and logical form of storytelling that KH had. It introduces characters, sets up the quest, foreshadows events, explains motivations and twists without going AHA LOL LOOK HOW SMART I AM, etc. Like how KH1 was about a bunch of Nomura Disney kids who go on a big adventure across Disney worlds to save the universe from an evil villain who wants to capture the hearts of all worlds, BbS is about a bunch of Nomura Disney jedi knights who go on a big adventure across Disney worlds in the twilight of the era of light.
The comparison between KH and MGS is actually very fitting, since KH = MGS, KH2 = MGS2 and BbS = MGS3.