There honestly is no real plot in Days. It's all character development of Roxas and Axel. To complain about the rest of the Organization not being developed is to be ignorant as to the entire purpose of the game. None of them matter whatsoever to the game aside from Saix. Xigbar doesn't even really matter to the overall story of the game, honestly. Xemnas barely appears in it and honestly isn't really that important either. It's supposed to be about Roxas and Axel and why they are friends. Xion just gave the game a plot to follow so that it wasn't literally "Mission -> Ice Cream -> Mission -> Ice Cream -> Day 358 -> Roxas saying "BYE GUYS!" -> End"
And for that, it's a wasted opportunity to expand and developed on the members that clearly need it. We could've have more in-depth with Roxas' relation to the Organization or at least more screen time for them, but hey, you've just proven that for me, Days is shit and a wasted opportunity.
And Xion's self-contained elements are connected to Birth By Sleep? Really? I fail to see this connection outside of that one scene towards the end. Everything about Xion is contained within Days. There are no secrets left about her at the end, really.
As I'm reading many theories on 'Replica = Unverse', then it's pretty much connected as far as I'm concerned, unofficially.