That's nice from a philosophical point of view, but like you said, none of that really goes anywhere in the game itself. All it does is add context and clarification to the main storyline, but it does not move anything along. 358's whole purpose was to flesh out what was already told in KHII, but it was not needed for story purposes. Appreciated, yes, because I think it's a good DS game, but certainly not important beyond Xion herself, who was retroactively created for 358, then killed off and therefore not significant beyond what happened in 358 itself.
Sounding important and being important are two very different things and in the end, all of what you mentioned were brought up in other games, 358 only expands on it. (Riku Replica in COM, the heart and the sense of self was mentioned in DDD but 358 doesn't really do anything with that and the Secret Reports all just add to the characters themselves. Again, appreciated, but not important since several of them were throwaways and most of them return in DDD as it is.) It does not further the plot because, by 358's release, we already knew what happened after and Roxas' time with the Organization was summarized and told in a way that got the point across, we didn't need a whole game to get the picture.
It's been said that the only reason Days was even made was just because Nomura wanted a title on handheld after COM and felt that adding to Roxas' story and adding onto Organization XIII was the smartest thing to do under the circumstances, which I agree. But everything you have mentioned either does not matter in the grand scheme of things or is usually also handled in the other games. (How Org.XIII works doesn't matter because it's not even the True version, you get everything you need to know out of it in KHII and DDD with regards to Sora and Xemnas' conversation about how Nobodies could grow hearts and Xemnas lied, along with which members actually returned as Xehanort clones - Xigbar, Saix - kind of paints the picture of who was really 'in' on Xehanort's plan, etc.; why Sora's memory took so long didn't need explaining, it's said by Namine in COM that it'd take some time, the details were never given and never needed to be given; what Riku did in between Days and KHII was made known in KHII, the only things we didn't know about was his interaction with Xion, a character retroactively created specifically for 358; and if what you mean by 'what the Organization actually wanted to get out of Castle Oblivion' is to extract Ventus, then that's little more than an addition to Xemnas' character that would already have been realized by KHIIFM's cutscene where he 'talks' with Aqua's armor, which gets the point across sufficiently on its own)
I agree with you that the character relationships and interactions are a huge draw for me, too, and 358 certainly adds on to all of that and fleshes everything out. When I call it 'useless', I mean only in the sense that you don't need to have played it to understand the main plot of the series up until this point. Some of what happened in 358 will no doubt be mentioned in KHIII if it comes up at all, but part of the reason Xion was the way she was was so that nobody would remember her, anyway. She could always come back (she sort of has already in DDD) but it doesn't seem extremely likely, just like I don't think we'll be seeing Data Sora or Riku anytime soon.
But what do I know? It's Nomura, 358 could also be the centerpiece of KHIII and I'm just talking out of my ass. My point is that, from KHI to DDD, the events in 358 can be best summarized as needless fluff, a means to an end in order to better characterize the characters that didn't have much screentime already and to further Roxas' character, all of which I feel are worthy goals to achieve, but not important.