As a developer lead, these features are extraordinarily useful. I can see the exact state of the card, and all its attached PRs across multiple repos, at a glance. I can jump into any of the PRs to contribute comments, update a review, make a review. I can make use of the PR assignment to assign different people to different parts of the overarching card (assign a different dev to the infrastructure PR, than for the front end PR, for instance) or to assign people to do the review while leaving the executing dev on the primary card.
It's a well designed UX that's trying to be exactly one thing: a highly functioning kanban board tightly integrated with Github. And it shows what good UX design can accomplish.
It's not perfect, but it's miles better than Jira and I'm feeling its lack having to move from Waffle to Jira.
To respond to the first point, I'm reacting to the fact that everything exists in common and must be associated rather than simply created. If someone's created a "Story Points" field already on another project, that's the one true "Story Points" field. If I want a different one for my project, I have to name it something else. And if other people have created a bunch of fields, you can quickly find yourself swimming in a mess.