I posted a thread about this a few days ago. My last post gives my thoughts about some strategic adjustments. Unfortunately, the thread died pretty quickly and no one really responded to it.
I have the same problem you have - I literally crush $0.50-$1 (and have for well over 10K hands - I think I give a rough count in the thread I linked to), and I have a decent number of $1-$2 hands (again over 10K), but my win rate is not even comparable (in BB / 100 that is).
One thought though - if I were to look at my hourly $ win rate for each limit it is probably higher at $0.50-$1, BUT when you factor in faster bonus clearance for $1-$2 this gap may narrow / cease to exist. I know someone pointed out the value of the bonus before me, but it's a really good point and bears repeating. Then if you factor in learning more and improving your game, $1-$2 now comes out ahead in terms of overall value. At least, that's how I'm looking at it.
Good luck.