Based on your latest post, I'd assume you supply the auto industry. I believe that all of the Big 3 now recognize registration to TS 16949 as an alternative to QS. Considering the future, I'd still suggest TS 16949 as a guide. (By the way, the TS reads almost identical in format to the existing QS. There are some additional requirements, though).
The real problem is that you're on the cusp with respect to the transition of TS 16949 to becoming a consistent pair to ISO 9000. My initial thought would be to be creative. Use ISO 9000 as a base document (it contains a cross reference to the old 1994 elements), then create a cross reference of the current TS requirements to the new ISO standard and fit the current TS requirements into the your system that is structured to fit ISO 9000:2000.
I'll admit I'm getting maybe a bit creative here myself, but if you're developing a new system it may be wise to start thinking in terms of where the future is going in the standards. I think you may have a number of different options here, and they probably depend on your company culture and the demands of your customers as much as where everything is going (or likely to go) in the future.
If you'd like to discuss this in greater detail outside the forum, you can e-mail me or give me a call…check my profile for contact info.