Hi Chuck,
Get ready for a deluge of suggestions and opinions. You are about to hear that Yamaha/Klipsh pairings sound "bright" and HTIB is not the right way to go and you should consider XYZ brand. Also, for $1000-$2000, there are litterally 1000's of options for you to chose from.
Bottom line, only you really know what you like. Listen to your options and compare with the competition. In recivers comparable to the Yamaha HTR-5650/5660 (RX-V540/640) you have the Onkyo 501/601, Denon 1603/1803 (or 04's), Harmon/Kardon 125/225, Pioneer Elite VSX-41 (or the non Elite 812/912), and a host of others (Marantz, NAD). In speakers, you also have just as much if not more choice.
Personally, I like the Yamaha. I actually purchased the Yamaha HTIB with the RX-V540 (same as the HTR-5650) and am happy with it but can see myself upgrading the sub when I move my home theater to a larger room in the basement. I didn't buy it at Best Buy because I couldn't test it there to my satisfaction. Luckily, a smaller retailer had it as an option and after listening to it and comparing it to a host of other options within my budget, the Yamaha was my winner. That doesn't mean it will be yours but you need to listen and make up your own mind. Also, I didn't want/need larger speakers, so I was happy with a sat/sub option (also easier to sell to the wife who didn't want speakers as "furniture".
Oh, also, don't worry to much about "specs". All of the receivers in this category will play basically the same sound formats. There has been many a debate in this forum with regards to watts per channel ratings and the like with no real conclusion. I hate to sound like a broken record, but make up your own mind by listening to your options.
JB