In what way does it compare unfavourably, exactly? A nine-car or 2x5 Azuma (never mind buffet-less GWR IETs) seats more passengers than an 11-car Pendolino. The toilets don't stink, etc.
If you lived in Lincoln, you might just take a different view about five-car sets - just the same as on a number of GWR services, that route will never support the extra costs of running nine-car, never mind 10-car trains all day.
Hull Trains and Grand Central, to take a couple of local examples, would not be viable operations if they were running long trains up and down half or more empty all the time. Franchised TOCs (and government-owned operators of last resort) are not immune from the same cost considerations.
And how exactly would splitting or joining a pair of sets at Leeds (during the period that has to allowed for reversal anyway) to serve, for example, both Skipton and Huddersfield pose a performance risk? We were told that the world would come to an end if splitting and joining happened for Cornish IETs at Plymouth on GWR, yet trains still seem to make it to and from Penzance somehow.