EWR said to accommodate the planned four services operating on the route per hour, the Bicester Road crossing would be forced to close for more than 32 minutes of every 60.
It said this would create “unacceptable” waiting times for users of the crossing and the “doubling” of traffic queues, as well as “significant safety concerns”.
The company has instead proposed the crossing be permanently closed, with a footbridge or underpass for pedestrians and cyclists installed in its place.
Under the plans, road traffic would be re-routed via existing roads.
Other proposals include improvements at pre-existing stations, and the use of partly electrified lines, with trains using hybrid batteries.