- burn-down / velocity charts: Teams use this at standups to make sure their sprint isn't drifting. That's why a burn-down should be tracked in hours and not points. With points, the data isn't actionable in a reasonable amount of time. The the team sees a problem, they might make use of a pre-determined emergency procedure to address it.
- retrospectives: Yeah most retrospectives are horrible. Retros should be like post rocket test - examine your telemetry deltas to see what changed (edge cases, governance,compliance, desgn, etc.) These conversations are not forced, but good teams always repeat the same data analysis unless they intentionally change it.
- poker sessions: Yeah this is totally misunderstood. Pointing stories is about snap reactions to comparing difficulties and complexity, and that's it, move on. Teams will tighten up estimates when they do an implementation plan in sprint planning. So they don't sweat estimates.
- daily stand-ups: The whole team is responsible for the sprint backlog, nothing is assigned, everything is volunteered. So if you're working on something that is going south, or you have some extra capacity, let your team know about it. The team will work together to scale capacity to get things done, which is how they can disappear on Friday afternoons.
- user stories and related tickets (eg in JIRA): Well yeah, Jira sucks. So do all the other major backlog tools. Jira gets addins, but the fundamental approach to backlog development hasn't changed in a decade. (I'm working on a soln from scratch, btw).
Also, user stories are meant to be work-items with enough signal so they can be executed with certainty in a sprint. So that means a lot of refinement to the left of the story must occur to get rid of the noise (epics to features to stories to tasks). Once a team says a story meets their definition of ready, that story can be scheduled for a (timely) sprint. Team members may be doing hard-core story refinement because of some technical hurdles, so their time outside of development during sprint can be pinned down with the team's capacity plan. BTW, capacity plans and implementation plans belong solely to the team. They're nobody else's business, including managers to CEOs.