I currently use notebooks to sort out my work flow.
May be this can be cleaned up and built-in to the App itself. Additionally if we can have a time tracking that is kicked of by two toolbar icons for 25 min focus timer and 5 min break timer. The logs for the timer are appended to the end of the note it self.
I implemented some of these techniques inside joplin just using folders with appropriate names. Eisenhower gets one folder with 4 sub-folders. Pomodoro doesn't work well because it's a process that relies on an external timer with 30 minutes; I guess it might work but there is too much effort involved in setting a timer for each 30 minute task, so I never bothered.
Maybe it's just my set up also. I have about 6000 tasks that regularly process on a yearly schedule.
You might propose some sort of a plug-in but I don't think it should be built into Joplin itself.