The full benefits may not be known until folks get units in their equipment racks and listen to them, because if it is as good as the Sherwood has been reported to be one key benefit will be sound quality (something that can't be spelled out in a feature list).
I always have a hard time finding good specs on Sony products, especially older ones (Sony's site has been what I consider a train wreck for years), so I can't really do a good comparison of features. I did get a little help from Google, though, and found a little information. Aside from the potential for having the system sound better, the DVI switching (not HDMI, although for video the two are essentially compatible with each other), auto-calibration (not EQ - it sounds like it'll set speaker distances, speaker trim settings, and probably whether the speakers should be large or small), and AV sync delay control are all features that could help justify an upgrade. There is also Pro Logic IIx, Dolby Headphone, a USB input for audio from your PC, and an extra component video input. There's the option of bass management on the 7.1 analog input. There may also be some benefits to the video switching, as I couldn't tell if the Sony supports converting composite and s-video signals to the component video output.
One last comment, though: the 990 is not a receiver, so if you are currently using the STR-DA4ES to power your speakers you would need to buy a power amp such as Outlaw's Model 7100 or 770 in order to use the 990.