Why does the cult leader want to destroy a city? What's he hoping to achieve by doing this? I find a good exercise for writing a believable villain is to write a logline from their perspective too.
No hero should be unwilling. They may be hesitant to start but ultimately they have to choose to step into Act II. The grandfather character can totally be reluctant, but as soon as the hero makes that decision to use their powers for good he HAS to stick to it.
Seems to be a lot of superpowers floating around in this world. Are there more people with powers? If so, why is it this 15 year old who has to do something? If not, how are you going to explain them? Every single superhero has an explanation for their abilities. They're aliens, bitten by a radioactive spider, built a suit, created by man, etc, etc. So far, I feel like we have to accept a world where someone can just be born with powers. Oh but his grandfather has powers too. Oh and this other dude. It starts getting a bit problematic in my head. How do you see this working?
In your revised version, the whole "disappearance of a family friend and injuring of his brother" really doesn't add anything. It doesn't seem to relate to the supervillain in any way either. Accepting his powers and going after the main villain is the climax of Act 1.
I really like the super boy and super grandpa dynamic so stick with this but figure out what's important, what's the main spine of the story and write the logline around that. I liked the way you ended with the whole "working ?with grandpa" bit... it adds a great comedic twist on the story and helps me imagine the tone of the film better. I hope that's what you were intending. Give us a 3 dimensional bad guy too.
Hope this helps.