For me personally the song is simply a love song:

Threw you the obvious and you flew
with it on your back, a name in your recollection,
thrown down among a million same.

***That Part of the song is about Maynard saying his love, or affection for someone and them just not disgarding it. He perhaps doesn't even tell them he likes them, they just don't see the signs***

difficult not to feel a little bit disappointed
and passed over
when I've looked right through
to see you naked and oblivious
and
you don't see me.
***This Part relates to the previous section, this person is obviously a friend to Maynard (naked and oblivious can be a metaphor for open) but despite this they still don't see Maynards love***

but I threw you the obvious
just to see if there's more behind the eyes
of a fallen angel,
***Maynard again referring to the obvious, this person is slipping in his esteem (fallen angel, meaning he/she was an angel previously)this is the beginning of the bitterness***

the eyes of a tragedy.
here I am expecting just a little bit
too much from the wounded.
but I see through it all
and see you.
***Perhaps this person he loves/likes has just experienced a tragedy, perhaps through love, a recent relationship split up (expecting too much from the wounded, he wants this person but they are still hurt from a relationship)****

so I threw you the obvious
to see what occurs behind the eyes of a fallen angel,
eyes of a tragedy.
***He threw the obvious to show love, to help this "fallen angel"***

oh well. apparently nothing.
you don't see me.
you don't see me at all.

***The final rejection, she doesn't see him at all, the worst feeling to someone can be that of being ignored by their love, unrequited love hurts the most****

So to me the song is about unrequited love, at least that's what it says to me.