hmmm I think you're putting too much into it than you have to. the fact that it made you think so much about his motivation and lack of focus convinces me that it left you a lot more than you bargained for, and should be thankful for it.
His reason for villany seems clear cut. Boy wanted fame and adoration and was rejected by the very example of his goals, so he as revenge constitutes, he goes after the dream crusher and all associated with it. It's very natural for someone with focused hate to become unfocused and starts to blame eveything else on that one reason, so with one fell swoop all his problems would be gone. or so he thinks.
As much as it seemed hokey to you, the Incredibles still had some of its morals directed towards a younger audience, but I'm glad it wasnt carefully laid out as some of the other kiddy fare. The theme about being special was brought up earlier when Elastibootymom told Dash that "everyone" was special, to which he answers "it's just another way of saying that no one is special". But at the end I believe the true moral was you have to use what you 'have' to make you stand out. Syndrome could have proved that he was a great superhero to Mr. Incredible, instead he used his genius and wealth for useless things. Fame and power is not an end result, it's a bonus.
now excuse me... I'm gonna go hug myself...