I agree for simple flat stitches. I work directly from the raw files through Bridge after doing some editing in CR and just saving them again as raw files. I am even able as you say, to make significant density changes in frames that are too dark, even when that is simply the way the scene was and get them to stitch fine with good transitions. Can Ptgui do that? I haven't worked with it much.
My workflow is to get as close as possible in ACR, then export individual frames as 16 bit tifs. Stitch with PTGui outputting a layered .psd or .psb. Then load into CS4, assign individual masked curve adjustment layers to most or all of the layers, equalize as needed, combine the individual adjustment layers with their corresponding images, select all the layers, and invoke auto-blend. It is important that individual masked adjustment layers be placed exactly above their associated image. Finally the size of most of my images forces me down to 8 bits/channel mode, but most of the equalization was already done in ACR or 16 bit mode and no large adjustments remain to be made at 8 bits.
This was a major revelation for me. I used to try to do all the image equalization in ACR by watching how the histograms animated as I flipped from image to image. The idea was that smooth histograms animations would equal smooth image transitions. That was pretty good but never really worked out anywhere near as good as the above.
BTW PTAssembler is another very good stitcher that supports far more esoteric possibilities than PTGui, but PTGui is a little easier to get into and runs in 64 bits on PC's.
