Due to the time issue personally I would pick one exercise and one stretch and use that time to perfect both. Keep the exercises basic and work on different forms and cadences. Ex.. Assign one day to be push up day. Then you pick and chose whether you want to work on explosiveness, time under tension (slow), different forms such as diamond, wide, dragon walks (spider mans), Hindu, etc. then work on stretching an area from either that workout or the previous day. This will allow you to keep track of your progress and will only take a few minutes to plan out a month or two.
Body weight exercises -
Upper-
Push ups
Bent over shoulder press
Rows
Neck "around the world"
Pull ups
Lower
Squats
Lunges
Split squats
Deadlift
Good mornings
Shrimp and pistol squats