I see, the natural question then is; Why two protagonists and not one? In what way does having more than one MC help the story?

The chain of events feels add-hock and the events themselves seam lacking a relation to each other.

By this I mean “…gaining special powers…” doesn’t flow logically in the world of the story on to them getting adopted and to motivate them to “… locate their remaining biological parents,” and “…evade capture from the agents that gave them their powers.”
For this chain of events to make perfect sense and leave the reader wanting more (as you can see from the logline) this story will need a lot of explaining. So if much explaining is needed in the logline this is indicative of the script having much explaining (likely exposition or direct address VO briefing etc…) as well. In story explanations = boring so best to reduce it as much as possible.

Also there have been many super power movies and specifically teenagers gaining super power movies at that. This means that you would need to work harder to make a kid with a super power original and interesting.

I recommend specifying the exact power the kids have because “super power” comes across as a generic description. This will help make these characters unique also best to relate the super power to their goal and give them an inner journey that relates as well.

e.g:
After an orphan with a fear of abandonment is made a clairvoyant by a secret government agency, he with the help of his new adopting family must find his parents whom he senses are alive and in trouble.

Putting the biological parents in “trouble” adds a ticking time bomb element and raises the stakes as well.

Hope this helps.