Bella has gotten that kind of upgrade, yeah... the very early builds didn't have her, and a lot of people missed her. I added three things to fix that:
1.Added more night time actions for Grassmarket (curries at the Khukuri, drinking and slice of life events at Grassmarket). I'd taught the player there's nothing to do there, which of course makes people not look there
2. He'll also talk to himself, a day or two after she's first available there, if he hasn't met her yet, saying "I should hit the grassmarket"
3. Finally, the follow-up meeting used to be just timed off the first meeting; I changed that so it became an Email, telling the player that she'd love to meet up with him later.
I could certainly add more little guides for that kind of stuff. Obviously that kind of thing doesn't have retroactive effect, and it's problem that I end up liking little side-characters enough that they get promoted into the main story (Bella, for example, was never supposed to be more than a side-character... I fell for her pretty fast, and so needed to make sure she was fully integrated). Similarly for Val and Matthew.