My main reasoning for picking the 2.1s over the R3s was that I actually started with the 2.1s as mains. I first purchased the 2.1s planning on evaluating them for the available 30 days and if I liked them adding the C2 and R2s (I was in a smallish on-campus apartment at the time), all in BC. I was so impressed with the 2.1s that I instead immediately added 4.1s as mains and a C3... Jon even extended some package pricing to me since I was returning so quickly.
A few years later (and a few months before I moved into the room pictured) I had the chance to sell my 4.1s and get a screaming deal on some b-stock 6.1s from OZ (just as great to work with as Jon Lane, just without the presence on the forums).... they were supposed to be BC, but I was accidentally shipped a brand-new pair in Rosewood instead. The return shipping and re-shipping would have cost more than the difference between the BC and Rosewood, so they let me keep them. This is how I settled on the 6.1/C3/2.1 system I have now. I'm actually somewhat lucky I ended up with 2.1s instead of R3s since mounting them in my room would be tough with the pitch of the ceiling.
As for the subwoofer, it's a pretty basic enclosure... short, deep, and wide and fit back into the dormer. You can just barely see it in the picture of the seating area. At the time it was covered in a beige vinyl that somewhat matched the wall color. It's since been refinished in a heavier-duty vinyl that matches the color of Rosewood Swans closely, though the grain is less prominent and it obviously lacks the laquer finish. I've used the same vinyl to wrap the legs of my equipment rack and the sides of my C3 so everything matches extremely well.
My system has been very evolutionary, but in its current incarnation things price out as around $650ish for the 6.1s (paid for B-Stock BC, got brand-new Rosewood), $330 for the C3 BC, $300 for the 2.1 BCs, $550 for the SR805 (open-box, Circuit City), and around $350 for the sub ($150 for the Avalanche driver on deep clearance, $150 for the BASH amp, and $50ish in building materials)... that comes to around $1630 total for the speakers/sub/receiver.
My only regret in all of this was the 4.1s. They're great speakers and would be the perfect choice for a lifestyle 2ch music system... but for HT, they didn't offer much of anything over the 2.1s and didn't have the amazing depth of the 6.1s (I used these without a sub for awhile and they were very impressive). If I were doing everything over again, I likely would have started with 2.1s front and back which would have given me the option to do 7.1 once I added the 6.1s (not that I would have given my room, but would have been a more logical progression).