How do you rate the various cities then? Hull is the tenth largest city in England - larger than Newcastle, larger than anything in Wales and above Aberdeen. Presumably you would take InterCity status from Nottingham and Derby too, because they are smaller than Bradford. Admittedly Sunderland is smaller still, but still comes out above Norwich. These are all major destinations.
I don't rate them, economic studies and geographers do (and I've studied it which is part of what I do but back to the point!..) I'm afraid Hull is no more than a town if you were to use global definitions on the inside of the industry. Neither is it particularly important economically. It should have an Intercity of course it should, but it isn't a major destination. The service frequency and loading purely in train terms also bares that out anyway.
Hull is not larger than Newcastle as when studying critical mass and where the major centre of employment is Sunderland is easily (even though locals would hate this and wouldn't agree) part of the Newcastle metro area. Over the years Newcastle is the dominant centre of employment and not Sunderland. Sunderland would not have what little standard of living it does if it were not for Newcastle. Cities are not measured today in the way you describe with old boundaries. Those studying city economics take no notice of it because it's no longer relevant just as Croydon was subsumed into London and acts as a suburb by every measure, as does sunderland to Newcastle.
Neither is it larger than anything in Wales as the critical mass and suburbs (that is continuous urbanised area connected to Cardiff) masses around 1.1 million people with very little measurable gap between that total and another 2 million people that splits between the rest of south Wales and Bristol (which is obviously its own place). Hull has no such population base around it that is as successful or as big.
All the places you mention deserve Intercity status but the overcrowding issue on Intercity comes from the ones that pass through 'the big O' which consists of a metro area stretching from Birmingham right around through Nottingham to Leeds and Manchester to Liverpool and this is where major overcrowding in the main comes from; the major population to population centres, NOT a major population cebtre to somewhere like Hull which passes through no other major population centres on the way.
To answer the other part of your comment, the cities in terms of the biggest centres of population attached to their respective central business districts break down as follows in 2010: 1) London 2) Manchester 3) Birmingham 4) Leeds 5) Glasgow 6) Liverpool 7) Sheffield 8) Bristol 9) Edinburgh 10) Nottingham. Hull in population and economic activity is still a further way down this list.
The northern cities of Liverpool, Manchester, Leeds, Sheffield, Nottingham/Derby, Leicester and Birmingham and almost Stoke are connected together to form a continuous mentropolitan area of some 17million people which creates very complex studies.
So when deciding where overcrowding is on trains there is correlation between where the trains go and how long they should be. My point is all the Intercity's that go through these major areas of business and population are always overcrowded and should be longer. Relating movement of people to these facts is imprtant which I hope HS2 will be 4 tracks south of Birmingham when it comes but I'm not holding my breath!