Of the things that could improve Days, a more central role for Namine would be at the top of my list. Throughout the game, she has to balance so many conflicting interests which impact her relationships with others, and in the midst of trying to establish her own moral center-- she and Axel are played off one another as compromised adherents to "duty" and "authority" and each of them are forced to make choices about whose orders they're going to follow. It's no coincidence that Xion meets with both of them in the late game after preparing herself for what she intends to do. Indeed, Namine's brief face-to-face with Xion (who is confronting similar but distinct questions of "fate" and "belonging") contains some of my favorite characterization in the KH series, with both girls coming to a common understanding derived from the lessons they've learned and what they've come to know about themselves: Namine having clearly grown from the prisoner who must necessarily entrap others (as in CoM) to an agent who is discovering how to work within the limits imposed upon her to offer characters something incredibly valuable which they aren't getting anywhere else; the truth. And not the neat, comfortable truth-as-fantasy she could craft for the people close to her and Sora, but the actual facts of the matter as they stand: in Days she's a stone's throw away from the girl who tells Roxas in KH2, with a total lack of finesse, "You were never supposed to exist." As well as the girl who actively subverts DiZ's will in order to go meet with Roxas, and defiantly reassures Roxas that his end is not the end.
Given that, it's difficult to imagine a version of Days where Namine's narrative doesn't run complementary to Xion's, but I would be interested to see a version where the parallels between her and Axel are more clearly defined. As with most things in Days, Namine's role contains a good deal of subtext, but she does have an arc and it would be cool to see it given further exploration. The biggest hurdle would be that having her meet with Roxas would be problematic: her statements and motivations in KH2 aside, Roxas doesn't consider himself bound to destiny or any greater universal movement and so her "truth", in addition to coming prematurely, wouldn't work in concert with his arc. Thematically, it would be pointless: nothing would come of it, since as DefiantHeart pointed out, Namine wouldn't be in a position to motivate Roxas. But it would still be great to get more insight into how she grapples with DiZ's dogmatism, and how that both plays into and is perhaps countered by both her guilt as well as her desire not just to repent, but to actively change and be a meaningful participant in the world around her. The relationship between Namine and DiZ, and the distinctions between her relative imprisonment under his watch and her definite imprisonment under that of the Organization, would be a neat thing to explore more, given how each represents a philosophical extreme in a game like Days which operates primarily in those imperfect grey areas. Namine, despite being a protagonist, is in a grey area herself: somewhere between existence and non-existence, reality and falsity, freedom and obligation (was the promise she made to Sora a consequence of her acts as a prisoner, or her first real choice as a free agent?). Days would be a great playground in which to run those ideas around.
Basically, I think that in order to do Days without Xion, the premise would have to be scrapped and I think the result would be Namine as the protagonist. Roxas could still have a role, but it would need to be decidedly background: maybe as someone Namine observes but never interacts with, and his arc would necessarily be relegated to those elements which contribute effectively to hers. I could see Namine witnessing the romance Axel and Roxas develop and wondering what it would take for her to have a similar connection with someone else. She might understand Axel's inability to commit to one course of action, or be entirely truthful, while recognizing her own sense of accountability on those fronts. It would be a good character study (albeit one I'd argue was affirmed less obviously in Days as is), but I'm not sure how it would play out in terms of a Beginning - Middle -End.