There would not have been sufficient units to over all the franchise commitments, including 8 car trains to Ely and the (delayed) frequency increase to King's Lynn.
Plus franchise commitments to run trains with air conditioning, wifi, power sockets on the Cambridge Express and on to the Fen Line.
The 365 could likely have been fitted with air conditioning etc if required, so I don't think that would have been a showstopper. The 387s do, on paper, have a slight advantage in being 110 mph capable - if ever allowed to work at that speed on GN.
But I think the real reasons were SDO, and simply that the numbers didn't match up. 29x387 plus 19x 365 equals 48 units, whereas there are only 40x 365. So if the whole 365 fleet was kept, there would have needed to be a top-up of something else - either more 700s (unpopular!), a smaller fleet of 387s, or something else. It might have been possible to make a case for keeping a rump fleet of 321s purely for peak services, which would have had an advantage in maximising seating capacity, but the down side would be performance. Any 365 or 321 option would also introduce a problem with short platforms and dispatch, so platform extensions would be necessary (as a minimum Baldock, Ashwell, Meldreth, Shepreth, Foxton, and in the longer term north of Cambridge), although that might not have been such a bad thing.
One way or other, the 387s are looking likely to be rather under-utilised from May, in that the daytime Ely/Kings Lynn fast service only requires something like 12x units to provide all-day 1tph KX to KL with 8 cars south of Cambridge and 1tph KX - Ely 8 cars throughout.
On a different note, my local newspaper has already published a list of 365 services from May, and mentions that local rail user groups have successfully pressurized to get 365s over 387s on certain services in order to maximise seating capacity. One wonders how true this is...