Though I haven't played BBS or 358/2 just yet, it didn't take much for me to find that those two did INDEED have a history together(TV Tropes kind of helped a bit there if the info given was reliable). It simply made sense to me. They were bitter enemies in KH2 and people like that usually started out as friends or even lovers. Not always, obviously, but it's pretty common. I call them the "Heavenly Bodies from Hell" and it looks like I was right. I prefer Axel with Demyx and Roxas, but I always did have Axel/Saix as sort of a "tugboat" relationship.
Only problem is that I'm WAY behind everyone else in the fandom, so I can't say much more because I don't want to spoil myself. I guess dealing RE: COM is inevitable since it's necessary to play that one first before going anywhere near 358/2 or BBS. So, wait for a very long awaited update. Good thing I don't have much of a concept of time because I know it's been awhile since I've played Re: COM.