I chose a long time ago to build a separate system for 2-channel. I have a Denon AVR and B&W 6 series speakers in the home theater system, and although I really need a 5-channel amp to finish it out, I'm not spending any more money on it until I am completely satisfied with my 2-channel system in the basement.
This is not a great option for everyone of course, because not everyone has a spare room for dedicated 2-channel. But most of the +/- $1000 pre-amps out there will best the pre-amp section in an AVR of the same or even slightly higher price point. This is definitely true in my case. And I almost bought an Onkyo, but found a great deal on a Denon at the last moment.
This is not a great option for everyone of course, because not everyone has a spare room for dedicated 2-channel. But most of the +/- $1000 pre-amps out there will best the pre-amp section in an AVR of the same or even slightly higher price point. This is definitely true in my case. And I almost bought an Onkyo, but found a great deal on a Denon at the last moment.