My amateur, and very quickly formulated analysis, would be something like this:

The speaker (not necessarily Thom Yorke) sees himself and his object of affection as belonging to two different worlds.  He is inordinately self-deprecating while praising her angelic complection.  He sucks, she's amazing.  This song very eloquently, and subtly, describes the feelings of a man who feels infinitely inadequate next to a woman he clearly adores.  The following line is the most telling of the song: "What the hell am I doing here?  I don't belong here."  He believes he's leading a sham life, undeserving of this woman who exists, by his perception, on another plane of beauty and perfection.  He's angry and frustrated for so many reasons:  1) he believes himself to be ugly and estranged, 2) he believes that he has enterred upon something he cannot sustain, namely, a relationship in which he is clearly the inferior element,  3)  all he wants to do is please her, he is at her mercy.  Hence, the line "whatever makes you happy, whatever you want."  

Alright, that was quick and much more could be said, but a friend is cooking dinner for me and I'm running late.  But one could spend years on Radiohead's lyrics.

P.S. the grammar is not always on target, but it doesn't have to be, it's a freakin song!  I was just writing about Creed's faulty grammar to point out the absurdity of all the comments like "Ooooh, you're so uneducated...blah blah blah. You can't use proper sentence structure...blah blah blah."  i hope the point has been made now