I can't agree more on this subject.
I just started my first game of SR4, got to the open world, and went to try and recreate the look I had in SR3. I had found an outfit with the pants I had while running around in the 50's thing and swapped to that for the time being until I got around to getting the parts.
Got to that point and went to every store on the map trying to find all the parts, I could not find the pants I had... Had to load up SR3 to look up the name, and searches on the net supplied me with my answer, the goth lyfe pants are only available in the outfit, and not as a separate piece.
Went looking to see if there were some mods that remedied this, anything I could find on the subject of adding clothing back in I had already installed.
This was greatly depressing to me, and I lost a lot of interest in playing it...
At least until this gets remedied, if ever.