Themes could be secret identity, courage, strength, commitment to mission, struggle to do the right thing, giftedness (how many times did I wish I had a superpower as a kid?), ...
I think since it is kid focused, I'll stay with positive themes rather than "struggle to do the right thing."
Identity -- The Incredibles seem to lose their identities when they stop using their gifts. They hide their identities to protect themselves and their families. The evil Syndrome (interesting SIN in the name) longs to be who he is not. This could be more about being who God created you to be as opposed to who you were not created to be, but sometimes long to be. Superman considers giving up his powers to marry Lois in Superman II but realizes he can't. Interesting how identity causes sacrifice as well. Scriptures: Psalm 139, Luke 4, Exodus 3, Joseph, Samson, Simon (renamed Peter - The Rock)
Giftedness -- Could use the Incredibles again. Batman doesn't have super powers, though could make the stretch, but why? Superman's powers are easier but almost too powerful. The Incredibles show a lot of different gifts and they are strongest when they work together. Hulk is more cursed than gifted. His gifts become strongest when he is furtherest from who he is. Seems to go the wrong direction. Scriptures -- 1 Corinthians 12, Romans ?? (Gifts), Sampson
Courage -- Somewhere in my lifetime, I became convinced that life was for the most part safe. I would read about times in history and maybe even other places in the world, but my life was safe. And for the most part (almost all), it has been safe. No illness. No accidents. No tragedy. But lately, seeing the world more broadly, I see a need for courage, to stand up for the one who isn't as strong, who wasn't given such a privileged position. Batman is courageous (or psychotic). Molded by the loss of his parents when he was young. Superman doesn't have that much to fear. So they are always threatening Lois. The Incredibles fear losing their children. Amazing how many kid shows (Nemo, Brother Bear, Beauty and the Beast, Lion King, Bug's Life, ...) start with very real tragedy and require courage from the unexpected hero.Scripture: Young David with Goliath (Don't lose your head), so maybe there is a better example than David.
Teamwork -- Could go with giftedness? Too many heroes work alone. That is why I like X-Men (darn copyright issues). Batman and Robin and even Batgirl. Again... the Incredibles. Scripture: David's Mighty Men
Anybody else with an idea?