Northampton is one of the big beneficiaries of Phase 1 released capacity, so hardly "neglected".
Firstly it was neglected in the NIC report, which is the topic of this thread, because Northampton wasn't included or considered despite it being within the East Midlands region.
Secondly, the major problem with rail if you live in Northampton is that there are no rail services to most of your nearby towns and cities - you can't get to Wellingborough, Kettering or Corby, despite them being significant county towns just along the A45, or Leicester or Nottingham just along the M1, or Market Harborough, or Daventry.
Northampton already has fast rail services down to London and to Birmingham, these services are already good, so HS2 Phase 1 releasing extra capacity on the WCML while it may provide some marginal benefits to the travelers using those services to existing destinations, doesn't address the more significant problem for Northampton which is the lack of rail routes and services to most of its adjacent towns and cities.