Chiltern's proposal in the 2002 franchise agreement was for a Marylebone to Oxford service, and by 2003 a report to the SRA determined that it would either be via Thame or via Bicester, and following detailed planning they chose the Bicester route for well documented reasons, so the original commitment (to Oxford) is delivered.
It may be that when first publicised people assumed it would be more likely to run via Thame, but that was not actually the wording of the 2002 Chiltern franchise agreement.
I linked to a report about the route decision making a couple of months ago:
http://www.chiltern-evergreen3.co.uk/uploads/09Sep2010/2.3.pdf