Ooh. That changes thing pretty significantly IMHO. As much as the amp section could be limiting the performance of your speakers, the preamp section of even a decent AVR can be just as detrimental and likely worse than the amps. If 2-channel audio is a priority I'd highly recommend getting either an integrated amp or separate stereo pre and amp to run the 3.5s for two channel, and then pick up a decent AVR that you can use for HT processing and for powering the center/rear channels. You simply run the front L/R preamp outs from the AVR to an unused or HT bypass input on the stereo pre or integrated amp. When you're doing HT you select that input on the stereo pre/integrated and match the volume to work with the other channels (happens automatically if your pre/integrated has a dedicated HT pass through input, but no big deal either way). This way you can have a dedicated 2-channel system within an HT setup without having any of the HT circuitry involved in stereo playback. Another benefit of going this route is you put more of your $$$ into where it matters most and can spend less on the AVR if you're not as critical about HT. Also, when technologies/connections change going forward you can swap out the relatively affordable AVR for a more current model and just keep using the stereo components as usual.
Incidentally, there were a few threads on this topic fairly recently where someone was looking to add a separate multichannel or stereo amp to replace the amp section of their AVR. What they found was that getting the AVR's preamp section out of the stereo picture was hugely impactful in the performance of their system -- even moreso than the amps. Sorry for being a little long winded, but given the quality of your speakers and interest in stereo I'd strongly recommend going this route. Best of luck.