Soundhound I applaud you and I absolutely agree with everything you said although I could not have explained or given the details as well. Stereo subs set up correctly in my system was the single best improvment in sound quality that I have made. (with the exeption of the speaker purchase) I do exactly as you said and have the subs directly beside the mains. I do have the LFE connected along with the main L/R channels but the controller for the subs allows me to defeat the LFE input and just use the mains signal. Your organ bass comment is right on because on of my favorite DVD-A's is Deep Purple and that Hammond sounds better with the stereo setup. No doubt in my mind.
SH I do have a question though. Do you think that maybe certain setups wouldn't benefit if the main L/R speakers are to close together? It seems a lot of people tuck the speakers as close to the monitor as possible which isn't how I have mine set.