Using it as a pre-amp, then sending it through the A/V amp seems to take some life away.I am not the least bit surprised. If you truly want the best of both worlds, I would ditch the Pioneer AVR entirely as that's what holding all your music back. The internal amps are too severely compromised to properly drive such a fine speakers as your Vandersteens (7 ohm nominal, 4 ohm minimum and only 86db sensitivity). No way are you going to realize their potential with an AVR.
You need true continuous wattage something that the AVR cannot deliver with its bogus specs. Look at a modern 2 channel integrated amp with a built-in DAC for digital needs and replace both the Pioneer AVR and vintage integrated with one unit that will properly drive your Vandersteens. NAD, Parasound, Yamaha are all making very good ones now. You'll be amazed.