I agree that the shared power supplies is the biggest reason separates start out with an advantage, but there are many other reasons.
A few that come to mind follow, but let me qualify that today's recievers are INCREDIBLE compared to those just a few years ago and when viewed with the task given! They have come a long way and do rival entry level separates (from quality companies). Would I let one in my home? NO, but it is probably due more to the fact that I am older and set in my ways than just pure sonic differences.
Remember, a receiver is a preamp, processor, tuner and multi-channel amplifier. Amps put out heat and need large heat sinks and/or fans to cool them. Few receivers have the physical space for proper heat sinks, nor do many have fans.
All electronic components change their electrical characteristics when they run outside of their designed operating range. Heat can cause power supplies to get noisy, add distortion and output unstable voltages that affect the entire food chain. Sonic characteristics are no longer the same.
Digital Signal Processors (DSP) are basically sophisticated computer chips that must not be subjected to too much heat or noise. Think about your PC and the heat sink and fans on just the processor chip. You don't get that luxury in receivers due to space compromises.
Cramming so much in to so little real estate creates physical separation limits forcing the video to be too close to the audio, the analog too close to the digital section. And then we put a tuner (RF device)close to the DSP and D/A converters (which we just raised the bandwidth on to support new formats!) just because we like challenges! Basic shielding principals have not changed since tuners were huge, separate boxes.
The solution? Put the hot, noisy amps in their own box with lots of cooling and their own power supply. Get ANY RF out of the box (tuners, RF modulators, demodulators) into their own. OK, now we have at least 3 boxes. Life is good. Life is separates! Hey, let's go to an extreme and take the video section and isolate it by having it's power supply turn off when in audio only processing. Or better yet, put it in it's own box! Now thats a system!
