What actually is the control score? is it the number of merits earned my commanders?

Roughly, yes. (Bonus merits earned by completing weekly tasks are purely personal, and it's possible that exploration/exobio counts slightly differently, but otherwise it seems to be that 1 merit earned = 1 merit to the controlled score)

So for each controlled system you get reported:
- total reinforcement merits for the system owner
- total undermining merits for everyone else combined
- downward pointing arrow on the progress bar indicating the start-of-week position
- upward pointing arrow on the progress bar indicating the current position
- blue or red chevrons between them (re)indicating the direction of difference this week

Note that the system the merit is paid in and the system the merit effects can be different for undermining actions: you steal PP supplies from settlements in an undermining system, and give them to your Power contact in a reinforcement system. You're given the merits while present in the reinforcement system but they're accounted to the progress bar in the undermining system.
 
My big question about control score and merits is if all merits from all activities count towards the control score or if it is only control activities that my power favors? Because if so, maintaining power with Kaine who only wants escape pods is gonna be a hell of a bad time.
 
My big question about control score and merits is if all merits from all activities count towards the control score or if it is only control activities that my power favors? Because if so, maintaining power with Kaine who only wants escape pods is gonna be a hell of a bad time.
All merits count. Preferred activities (those listed) get a 50% bonus to both personal and system activity - which is nice, but not essential in most cases.

(Note that since my earlier post in this thread, Frontier have separated personal and system merits so that most activities give 4x as many personal merits as system ones. Hopefully this is just a temporary fix while they work on bigger balancing issues and it'll be back to 1:1 later)
 
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