Well they did do something very cool with Isabella's storyline: she was resurrected by Nurgle to taunt her husband. Possesed by a demon she lead Nurgle's army into battle and beat up Mannfred and Vlad. The End Times really had some nice plot twists.
This wasn't Isabella doing anything. She was controlled by Vlad, then she was controlled by a nurgle demon to make vlad feel bad, then vlad sacrificed himself to save her only for her to spend the rest of the time between that and the end of the world unconscious. At no point did Isabella ever actually do anything ov her own volition, at no point did we get to see what she actually thought or felt or who she was as a character. That's not a major criticism or anything, a lot of stuff was going on and their corner of the narrative was focused on the well known and well liked Vlad, and in particular on giving his story a more satisfying ending than 'betrayed by warhammer starscream before getting pushed onto some spikes by some empire guy. That's all fair and good, and I think the writers of the end times narrative really succeeded in their goals with that particular plot thread.
That's also why I'm happy to leave Vlad's story as it is. They did a good job with it. There is absolutely nothing for Vlad to be doing in the AoS setting that would justify undoing that very satisfying conclusion. I'd love to see him back, but specifically in the upcoming Warhammer Old World game. The starting setting of that game, as I understand it, will be a couple centuries before the Vampire Wars, but if it's successful there's no reason why it couldn't progress over time and maybe in an edition or two make the Vampire Wars their core narrative, covering them in more mechanical detail than Oldhammer ever did. Could you imagine an in depth, forgeworld horus heresy style campaign book or set of campaign books laying out the individual battles of Vlad's campaign in high detail? Would be amazing.
Back to Isabella, though, I think where Vlad's story left off would have been an ideal spot to let Isabella's own story start. You have Nurgle breaking Vlad's hold on her and Vlad breaking Nurgle's hold on her, together leaving her theoretically free to think for herself for the first time basically ever. You have the nurgle daemon's possession dredging up and forcing her to confront just how controlling Vlad was, just how little her own feelings for him could be trusted, how much of it was just Vlad projecting his own vanity back at himself through her as a proxy. But then you have Vlad sacrificing himself to save her, showing that at least on some level he did care about her, further complicating her emotions. So what is she going to do now, with no direct masters? The last time she was on her own she killed herself to be with Vlad in death, but even if she hadn't been forced to face how manipulated her feelings for Vlad were, after Vlad killing himself to save her, killing herself again would be throwing his sacrifice away. That's a great launching point for a self realization narrative that could be taken in any number of directions. You could have her go on a revenge fueled rampage against Mannfred both for betraying vlad and for disrespecting her so badly. You could have her take up vlad's mantle and memory as a new mortarch of shadow. You could have her reject vampires, the undead, and nagash altogether, and sign up with sigmar instead. You could have her be rivals with, or, better, friends and co-conspirators with Neferata. and the direction the writers seem to have chosen for her is 'none at all', which really does imply that they never saw any point or potential to her character besides being a source of man-angst for Vlad, and imo that's kind of a waste.
