HDMI offers support for the new high-res audio formats - it's the best choice for digital audio with Blu-ray. Sound quality also depends on the equipment being used, though. We haven't heard the 997 yet, so it's real hard to say how it's analog performance will match up to the BDP-83's analog performance through the 990. You will have access to Trinnov with an HDMI connection to the 997.
I saw a post this morning on AVS from someone with a Yamaha receiver (a recently mid-level model with HDMI) and a BDP-83. He'd been using HDMI for a week or two and been very pleased, but based on some ongoing discussion about the BDP-83's analog section he hooked that up as well and tried it. He found that the sound quality via analog was clearly better than via HDMI, which is because the BDP-83's analog section is better than his receiver's analog section. Without having heard the 997, I would guess that the BDP-83 could match up fairly closely with the 997 for analog performance, but you won't be able to use Trinnov on the 997 via analog.