Yes there is a very significant difference between Pro-Logic and DD/DTS. Pro-Logic is not discrete in the surrounds, which means no directionality in the rear. The surrounds are also limited in frequency range. You can pick up a very inexpensive DD/DTS receiver today, there is really no reason not to have digital audio.
Second, if HTiB is the way you wish to go, I would recommend the Onkyo systems. They come with real receivers and can be used as building blocks for a future system, given that the speakers are the weakest link. Here's one with HDMI for less that $800:
http://www.circuitcity.com/ssm/Onkyo...oductDetail.do