Yeah in my case I got rid of my crt awhile ago, so I dont have much of a choice haha. Still my biggest complaint besides the varying loss of quality is how in the case of persona 3, theres no screen adjust option, so ive got a half an inch or so on the left thats just black...damn is that annoying.
The black bars on the side are there to prevent the picture from clipping off when playing them on CRTs. I play ps2 games in 4:3 so I don't even notice the black bars (since the widescreen part is black).