Specifically, I'm hoping for more plot related connections to the Shining Lady conflict. I'm not asking for anything ridiculously huge (I get that including things like the SoD companions would take a LOT of work). But it would be nice to be able to acknowledge that the SoD portion of the saga happened. Maybe a line of dialogue with Jaheira in the beginning of the game where you can point out that Irenicus is the man who framed you for Skie's murder? I would gladly do a no-story mode run of Chateau Irenicus with all my new characters just for that one line of dialogue. And I HATE that place.
Speaking of Skie, I would love a chance to wrap up her storyline in BG2. Nothing too crazy, but it would be nice to find her dagger somewhere (Chateau Irenicus? Spellhold?). Afterward, we could send it and a letter to Duke Silvershield via messenger and tie up that loose end. Maybe we could even get a letter from a revived Skie in ToB, thanking us for our help and explaining that she's cleared our name in Baldur's Gate. (I don't know if that would work lore-wise, but I REALLY want to save her. She worked too hard to become independent during SoD just to spend the rest of eternity wasting away in a dagger, dammit!)
What about all of you? Is there anything you'd like to see referenced from SoD's plot?