Not parent, but my biggest challenge is some v3 APIs are not there in v4 yet. For example, activity and notifications (https://docs.github.com/en/rest/activity/notifications) is something I'm still looking forward to, but forced to keep using REST until it becomes available via GraphQL.

The pagination point is described well in nearby comments. It only applies when attempting to paginate across more than 1 dimension at once, like "get all pages of comments in an issue, and all pages of reactions for each comment".