Rolling stock and traincrew are not the most important constraint, which is train paths especially at Ely and Peterborough. Don't forget that we are not just talking passenger trains here, there is a lot of freight than needs train paths too.
When train paths are the constraint what is required is fewer longer trains not more short trains. It would be nice if every route had 2tph, including Ely-Kings Lynn. Norwich, Ipswich and Cambridge would all like through trains to Peterborough, but there isn't room for them all.
More through services could be retained by portion working, but that seems to be out of favour. Another way is alternating destinations like the North East/South west timetable did 40-50 years ago, but that seems to be out of favour too. Otherwise, fewer longer trains means sacrificing some through journeys, but that can be compensated by an overall increase in capacity. Which nodes are linked by direct trains is a choice, and the choices made 30 years ago are not necessarily still appropriate now.