Hi Brett,
In terms of your general complaint, it doesn't matter what software you use to process - every astro image is different and requires different tweaks and techniques. That said, the PI interface and workflow doesn't suit everyone.
I use a variety of techniques for colour calibration. If you don't have a galaxy to use as a white reference you can try using the whole image with structure detection enabled. This will use the combination of all the stars in the image as the white reference. This can give decent results so long as you're not imaging through dust. Another simple technique is just to line up the R, G and B peaks in the histogram (or try an unlinked STF stretch.) If you're really keen another option is to use eXcalibrator (
http://bf-astro.com/excalibrator/excalibrator.htm). It gives good results but requires plate solving and a bit of mucking around.
Cheers,
Rick.