There was plenty of emotional pull, it just wasn't from the Scions. This expansion turned what was otherwise mustache-twirling blackguards into mildly sympathetic characters. There's no way to condone genocide, of course, but it made you understand what they were trying to accomplish. They want to save their world the same way the WoL did. This isn't my point, though, this is in response to yours regarding emotional pull.
As for Y'shtola being plucked from the Lifestream a second time, I would've sworn they addressed why she didn't have any adverse effects that time through dialogue, but I'll have to go and recheck. That's actually a solid point.
The Exarch not truly dying isn't a plothole. Again, they used a well-established plot device from ARR and they've demonstrated that anybody can do it with the right resources. A dark crystal or something similar.
Shadowbringers is still quite dark even without character death--way darker compared to the rest of the expansions. Tesleen's transformation, Vauthry making Kai-Shirr flay himself to feed Sin Eaters, the inhabitants of the slums of Kholusia being fed the previous inhabitants of Eulmore who became Sin Eaters so that Vauthry had a wider range of enthrallment over them over time, the WoL slowly dying through the latter half of the expansion, the WoL and the rest of the Scions actually dying if they didn't go to the First thanks to Urianger's vision. These are just a few examples.
Lastly, in regards to the Exarch, you are quite literally his favorite superhero. He tells you as much throughout the story and it's not so farfetched that, in what he thought was to be his final moments, he wanted to spend those last few moments with you because he resigned himself to dying. You can call it an annoying fanboy moment, that's fine, but the fact that he went through hell and high water to save you by getting you to the First and then took the time to express how important you are to them is, yeah, a soft moment that added a lot to his character development. No one else went through the lengths he did. I'll level with you in that I don't actually mind character death--it does add some interesting new dynamics to a story, but it's not always necessary. Other than that, we'll agree to disagree.