The moral of The Incredibles
"some people are just better than others, deal with it". It's "don't throw away your life & family in pursuit of glory." Bob & Syndrome both exemplify this, one learning his lesson, the other ignoring it.
Bob is a former superhero, forced into retirement when the public outrage over supers becomes too much for the government to handle. He can't stand having to live a normal life, where he's backwards & levels below everyone else. He doesn't connect with his kids, is forced to answer the whims of his shifty boss, & often sneaks out with his fellow super buddy for late-night rescuing thrills. When he gets the chance to resume hero work for a mysterious organization, Bob jumps at the call & can't believe his luck. But he's forced to realize the consequences when he discovers he's been furthering a villain's plans, & in the process put his family in danger.
Bob's turning point manifests when they're all captured and he's confesses how he was too caught up in the past: "I've been a lousy father, blind to what I have. So obsessed with being undervalued that I undervalued all of you. You are my greatest adventure, and I almost missed it."
Compare Syndrome. He wants the same glory that Mr. Incredible had, cares nothing about civilians, & views hero work as a fame ticket. He's
the one who's misinterpreted the message to be "deal with living with people who are better than you". He wants to overcome that, & could do so. But he would be a horrible hero if he succeeded (Just look at how he threw that truck in the city!) He threw his whole childhood away, his inventive genius, & even his perhaps girlfriend away just so he could be an idol. His motive is glory, not equality. The result? He underestimates those who are just pawns to him, so both Mirage & the Omnidroid take steps to lock his fall.
The film has multiple character development lines, Violet's shyness, Dash's vanity, etc, so it's easy to miss Bob's too. But so it's clear his arc is the true message of The Incredibles
, since Brad Bird wrote it as a reflection of his own career
. So if there's any moral it wanted to send it, it was that one about family & not that "the supers should rule us."