Don't forget that Flybe started talking about routes from SEN at much they same time as they were developing their NWI hub. They presumably did not think that there would be a great deal of overlap at that time.
I suppose if you live in, say, Colchester you might consider NWI as an alternative to SEN but my experience as a traveller is that I choose the departure point that offers me the most convenient schedule and the least likely hassle parking, at check-in and security etc. provided it is within a roughly similar driving distance. If I lived in Colchester I would use SEN in preference to STN or NWI if it offered me the same destination with comparable scheduling.