How does the protagonist system work? Do you get to choose who to play as or does it just play them both automatically?
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To answer your original question, it is automatic. It switches as the story dictates, though I try to avoid needlessly head-hopping.
Just to clear up something Starset wrote, Luke (the female protagonists ex) is not a character you control, which I admittedly made him seem like by giving him a choice. It could've been better implemented. Aside from the main male and female protagonists, the rest of VN was supposed to take on a third person omniscient POV for the other characters, while the protagonists took on something of a pseudo third-person limited.
Without spoiling too much, Luke is connected to something revealed at the end of this first release, and thus the female protagonist (Rainn). The choice made with Luke directly affects whether he has a chance to get back together with the female protagonist (player/viewers choice, of course.) or not. The reason maybe be obvious to some.
I felt it was necessary to make the connection early, so I didn't have to infodump on everyone later on. That being said, Luke won't be appearing again for some time as it's currently a side story to the main storyline (but will eventually become one of many conflicts.). Hope that clears everything up for you (and anyone possibly reading.). :)
TL;DR: It is automatic and Luke is not a playable protagonist.