As stated numerous times before, there's no clear-cut answer to whether HDMI or analog is better as it depends entirely on what's at the other end of the cable(s). In your case, you mentioned that you've found that Audyssey makes a pretty big improvement in the sound - that means you would want to use HDMI instead of analog. You also have a mix of 2 different brands of speakers. My advice, as I stated before, is to get a BDP-103 and put the extra money into upgrading your speakers so at least the front three speakers are all from the same brand and intended to be used together. IMO, that's a much better way to spend the extra $700.
What's wrong with having 2 brand's of speakers..... elaborate please.