Initially both EWR and Marylebone are 2tph, but EWR would ramp up with the extensions to Bedford and then Cambridge. So if you want to keep all the EWR together say for interworking, then it's the Marylebone for the branch.Chiltern (or that service group at least) makes sense because they have trains terminating at Oxford from the north end of the station, so they're the obvious pick to extend.
In some ways the MK trains make more sense than the Marylebone ones, but it's 6 and two threes, really.
MK has the potential to import delays to/from the WCML, if you're keeping EWR to the bays then that can be alleviated.
If Oxford is congested, then any additional services being sent through it are going to be an issue, whether they're heading for MK or London. Oxford doesn't have any south facing bays, so there's not really any scope for Cowley to be a shuttle.