I use my HT setup as my 2-channel setup, so I can only comment from that perspective. My end goals are the same as yours.
I'm personally very happy and satisfied. I use an Anthem with ARC for both 2 channel and HT setup. My only comments on your thoughts are:
1) Don't skimp on the sub. Listen and get the best sub you can afford. It makes a huge difference. This is especially the case if your speakers only go down to 40-30hz. I'm very, very happy with the way my sub interplays with both music and movies. My Anthem allows me to have custom settings for music with the sub crossover, etc. and also totally different settings for movies. Thus, I get the best of both worlds.
2) I can respect your thoughts for a separate preamp just for 2-channel. If you have the cash, go for it. That's all a matter of personal preference. Don't know where you stand on room correction, but I've become a huge proponent since i've seen what it has done in my room. I spent quite a bit of time positioning and testing my speakers. Room correction took it to another great level as the room was playing an effect as all rooms do.
3) I would not skimp on the "basic" AVR (again, don't now what you're calling a basic AVR). If you're serious about your HT experience you'll regret going with a basic one
4) Unless you have an unlimited budget, I'd do one setup and spend the $$$ to find a set of speakers that will do your 2-channel and HT. There are many models and companies that do this and do it very well if not spectacularly well. NOLA, Revel, Focal, ADAM, B&W are but a few that I would strongly suggest you listen to. In fact, the NOLA speakers are some of the most musical and dynamic speakers out there that do an absolutely stunning job with 2-channel and also with home theater. The ribbon tweeter, and open baffle is to die for. The dynamics and also depth of stage you get is wonderful. If you can listen to the NOLA Baby Grands, your jaw will drop. Ditto with the Revels and the Focal Utopia series. You have plenty of options out there.
5) If cost is no object, then look at Audio Research products that will satisfy your tube itch and also be able to do HT and 2 channel with equal authority and grace.
6) i agree with your ideas about the quality progression from fronts to surrounds; however, try to stay in the same brand or speaker family. Otherwise you will notice a difference. I don't care what anyone else says, if you have a high-end setup, you will notice the timbre difference with different speakers from different manufacturers.
Finally, have fun.