Am I missing something?
You're both missing some things, yes.
The example is assuming that Omni-Man is helplessly standing there taking the concentrated fire by the minions, and that he would let the minions even exist after his turn in the round. He's got his actions plus the Quickness power. He could pretty easily dodge any typical minion attacks (and not get hit at all in the first place since any successes he rolls wipes off their successes). So even if three groups attacked, he could use both his actions to dodge to eliminate two of the groups even hitting him, and he could use Quickness to negate the third minion group. Even if he wants to actually use his actions to go on the offensive in a round where he gets a lower initiative card, he can get to them and attack with a slugfest attack of 10 dice (very likely success plus Double Damage, even if the minions dodge), and a slugfest damage of 8. If he uses Quickness, he's taking out two of the three groups in one turn and they'll never be able to attack him again.
Omni-Man (and the other Viltrumites, Battle Beast, etc.) would also be okay against a nuclear missile, but it would give them more trouble than the minions since the 12 Damage listed doesn't give an attack roll. That would conceivably be a computer-assisted targeting system with 10+ dice. Not impossible to dodge, but much harder.
To sum up, there's more to how the game plays than "stand there and let these soldiers take you down." For the really powerful characters, they're still going to be unbothered by normal soldiers, but feel a little more pressure against a nuke.
I've played several sessions with my group at this point (as a player and as a GM), and the game really has a nice feel to it, especially when it comes to scale. It made our group's players feel like superheroes while still having the possibility of feeling threatened by bigger threats.