I do think it's kinda amusing. The message I see in the movie is so blatantly, over-the-top, ham-fistedly obvious, and it kinda boggles my mind to see people coming away with another message.
I partly agree with this. The movie does have several obvious messages, and one is definately what you and most people have picked up on. On the other hand, I think the movie works at a great many levels on a great many themes, and so I'm not surprised that you and someone else see different themes as central.
Syndrome's threat, "When everyone is special, then no one will be.", is one of those things that has several layers of meaning available from the context and depending on how you read 'special'.
The salient facts are:
1) The world of mid-movie is already a world where everyone is special (celebrating 4th grade 'graduation') but no one is allowed to be special (Dash and Violet must not only hide their powers but be ashamed of them. Helen must encourage her children not to excel. Bob is not allowed to help anyone and is continually victimized by people who are themselves pathetic, self-interested, and untalented.). This world is horrible and oppressive for everyone.
2) Syndrome's intention of releasing his inventions is clearly intended to continue this oppression, not to alleviate people from it. Syndrome's words are a threat because he's not threatening to release anyone from oppression but to deepen their general bondage.
3) Syndrome's threat is not fully credible because he's clearly a hypocrit. He is obviously not someone who cares for others and wants to help enable their greatness. He has always used his talents to subjegate others and enable oppressors. He's a weapons merchant that sells to people who use force to demand respect, and force and threats are the currency he deals in.
4) Syndrome is special himself. Sure, he's not special in exactly the way that the heroes are, but as a gadgeteer his potentially a 'great person' capable of helping others and advancing the general well-being of the world. But compare him to the good gadgeteer. Edna shares her technology. Syndrome keeps for himself. Edna empowers others. Syndrome empowers himself. Edna empowers heros. Syndrome empowers oppressive regimes. Edna encourages others. Syndrome uses others. Ednas goal is to make others look good. Syndromes goal is to make others look bad. Edna is motivated by her art - she neither wants nor needs approval. Syndrome is motivated by solely by desire for others approval. Buddy could be a hero. But Buddy lacks the heroic motivation.
But I'm making this sound more Randian than it is. The movie doesn't in fact advance objectivism, but something a good deal more complex and nuanced.
If there is one message you ought to take from the film that is central to what it wants to convey it is, "No capes."