You can still get Dolby 5.1 from DirecTV HD service without HDMI - coaxial or optical is all you need. Frankly, moving to a digital output if possible is likely to be a significant improvement over stereo analog output. Also keep in mind that PLIIx-Music offers some controls that alter how the center and surrounds behave, although nothing that will create a delay in the surrounds. I'm not a real big fan of NEO:6 either, so I'd tend to focus my attention on PLII over NEO:6.
It's hard to speak definitively when comparing a receiver I haven't heard to a processor that doesn't exist yet, but I can theorize a bit. Mainly, you will gain better audio quality due to the DAC's and overall design of the 997 compared to a mass-market receiver like your Yamaha. That will be most apparent on music, but you'll hear it on movies too. There are different features to consider as well, but it's the audio quality that is the biggest factor in differentiating a product like the Model 997 from receivers like the 2500 or 3900. You'll give up those "popular" DSP modes (which Outlaw quit supporting based on customer input back in 2000 or 2001 when the Model 950 was in development), but it's not something that I've missed at all.