The obvious missing link is Northampton to Wellingborough, mostly for freight. If electrified, along with the MML to link Doncaster / Wakefield / York / Leeds, you're looking at a new electric spine from Daventry to the East Midlands and the North. It also opens up linkage from Leicester, Market Harborough, Kettering and Wellingborough to Northampton, connectivity to Milton Keynes as a bonus.
The north curve at Bletchley makes reasonable sense to me. In the future, with less main line non-stop and "Pendolino" passenger traffic, there will be capacity for freight via Weedon and fast line "Regional" stuff, so expect more trains to arrive on Platform 5 to go to Northampton, and more stuff on the up fast from Hanslope.
If this is the case, you reasonably open up Milton Keynes to a half-hourly service to Cambridge, and a half-hourly service to Oxford. They won't be the same services, but people would connect at MK. You then just thumb an hourly service from Aylesbury 'direct' over the Bedford-Bletchley, and you can extend that to wherever you so desire.