You'll have a better system if you go 2.1! You don't need all those extra speakers, amps, etc. If you spend your money on a really good stereo setup you will blow away any AV setup for the same cost! All those extra speakers will require major room treatments to sound any good at all.

disclaimer: I like music on a stereo much better than watching TV. The pictures are better!

Chris,
if you're looking for a great home theater. The first thing, I would do is go out and audition speakers for your mains. Find the sound that you like best first and foremost. I see you have Sonus Faber on your list which I am quite impressed with and amd current a fan and owner of Vienna Acoustic speakers (I would recommend giving them a listen too) As for a system in that price range, I would reccomend looking at NAD or Arcam Pre-amp/processors, and power amps. Vienna Acoustics Beethoven Baby Grands (Mains), Mozart Grands (Surrounds), Maestro (Center), and a REL B1 for your subwoofer or what REL calls "Sub-bass system". That would be an AMAZING set up especially if there is a dealer close to you that has gone to Sumiko's Masters and Star Training. Sumiko, importer and distributor in the U.S. for Vienna Acoustics and Sonus Faber, has a training they do to preform proper speaker placement and adjustments to your gear to get it tuned in for almost any room enviroment. And a System like that would set you back about $16k.

But that's just my opinion on a great home theater system. Ultimately, you're going to have to go listen to speakers for the mains to see the sound you like and then go from there for the rest of the matching speakers.