The route should have never included Bedford Midland, and possibly not MKC.
There should have been a new station near the Interchange retail park connecting the MML and EWR lines, creating new travel opportunities for Wixams residents and Interchange shoppers, and new connections onto both mainlines. At "Bedford South Parkway" you would only be waiting 15 minutes at most for a Thameslink service either north to Bedford or south to Luton/St Albans.
I'm not familiar with the Bletchley end but I suspect there are at least 4tph connecting Bletchley to MKC, so again no more than a 15 minute wait for a connection.
EWR should have focused on high speed between Oxford, Cambridge and connections to the various mainlines it connects (Chiltern, West Coast, Midland Mainline/Thameslink and East Coast).
The very small stations between Bletchley and Bedford should be closed to speed up the line and journeys on it. No-one needs Kempston Hardwick station.
And then run fast services Oxford <> Bicester <> Bletchley <> Bedford South Parkway <> Cambridge, and stopping services taking in Winslow, St Neots and the remaining Marston Valley stations in actual towns.
Bedford South Parkway becomes a stop on Midland Mainline Electrics to/from Corby and all Thameslink services.
Build a massive car park at Bedford South Parkway to relieve the (pre-Covid) parking issues at Bedford and Flitwick, and replace the Park and Ride facility at Elstow.
Wrong way around - not MKC because that creates a 10-15 minute overhead on EWR end to end journey times along a congested bit of the WCML.
Bedford was less clear cut, because a new route is needed to the East of Bedford and logically a number of those made sense to include Bedford Midland as part of that. As it happens they've chosen the one which heads right through Bedford Midland - which is probably the right choice given the objectives of EWR.