Colors should be the same on VGA or HDMI in an ideal world. Maybe the Xbox 360 is different and introduces something else into the mix affecting the colors.
If the token is turned on, HDMI will be required for HD-DVD on the 360. That said, I wouldn't even factor it in. The odds on this happening in anything other than the long-term are infinitesimal. They created their strategy and are moving forward, they do not want to alienate the very large group of early adopters who paid large dollars for displays which lack HDMI/DVI - this includes some very high end displays including CRT front projection.
1080i can carry a film based 1080p source and be deinterlaced back to 1080p with no loss. I would not concern myself with this. For games, the display will also deinterlace and display progressively.
I would not stress over the connections - it really should not be some mega night and day difference. Get the system you want that plays the games you want to play. For the most part they are very comparable from a capability standpoint and PS3 will get more games over time. Go to the store, buy one and try it - maybe buy both and return the one you don't like. Try the 360 with component as well as VGA - 1080p won't really matter so go with the connection you like best.
Panasonic 65" VT60 (calibrated by Jeff Meier), Marantz 6005, Kef Q towers/rears Kef Reference center, Win 7 Pro with XBMC, Harmony Ultimate One
Xbox Live: Arbitrage XXL