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The OASIS organization is now solidly behind ebXML Messaging Services (aka ebMS), and a new draft was produced on Nov. 30, 2005, just about three short months ago. I think it's not an unsafe bet (notice the double negative? It's a hesitant acknowledgement/recommendation to be sure) and also one that's more likely to produce both internally usable and externally sharable results than a "roll your own" implementation built atop the raw building blocks of SOAP and WSDL. That said, it's far from clear that ebMS offers any distinct advantages over BPEL (also the subject of an emerging OASIS specification, ironically enough) and doesn't have the throw weight of IBM fully behind it, either.
Were I in your shoes, I would ask my customer if they had a compelling reason to go one way or the other. If partnerships or alliances don't dictate the choice for them and you, I'm inclined to back your play and tell you to go ahead with BPEL. It has a lot more supporting infrastructure at this point and (from what I can tell) is the focus for lots more actual implementations and adoptions as well.
If all else fails, cheer yourself up with this statement of fact: Any sufficiently rigorous XML syntax/structure (and both sets of markup qualify) can be transformed into something else equally arbitrary and rigorous using XSLT in the future! Just hope like heck it will be a one-way-only transform!
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