The Hero's theme is only really featured three times. Once after the first battle sequence, the pause, and then the melody is first presented. (F-C F-Eb) is the main motif of the theme. The second time is at around 3:29, where the glockenspiel, low strings, and piano create a dreamlike sound that is meant to be the Hero succombing to the Villian's powers or whatever. The melody transforms four times with the different soli (sax, violin, flute and trumpet), and each one of the melodies changes the key, and in each key, there are actually four keys going at once. A little polytonality that actually doesn't sound horrible! The third time would be at 6:35, where the trumpets start calling, then the woodwinds honk out the signature motif (F-C F-Eb) thing, which is interlaced (flutes) with the (F-Eb-Gb) motif from the Villian's theme. That starts into (6:46) the last battle(which I agree is not nearly long enough...I was running out of time), which has both motifs going on alltogether. Also, at 7:14, the saxes and strings have the signature Hero motif again, this time in C (C-G-C-Bb), which then the woodwinds turn into the Love Interest's theme, with the (B- A-G#-B- AG#F# ).
Anyway, there's me defending my piece.
I agree it's not perfect, and Sean's right, I did not deal with the Hero's theme quite enough. But, I did include it other places than the first appearance, it is just slightly hidden. Oh well. I did my best. Oh, and Sean, you mention glissandi in the Hero's theme...there is none. That's the Villian's theme. Ok, here I have attached a pdf of the themes, maybe that'll make this easier to understand.
And don't worry, buddy, I listen to many soundtracks and read many comic books as well. I know what you mean!
Also, I have attached the MIDI for my piece.