In time, the North will gradually get to use the 4-car stock effectively. It may be by SDO or lengthening platforms where 6-car trains can currently be used to 8-car to handle growth.
It's not just lengthening platforms though.
As already mentioned Network Rail spent £12m at Salford Crescent for the purpose of 6 car 185s stopping there, as there were a lot of infrastructure changes required to allow for longer platforms.
Alliance Rail looked at stopping their open access services at Winsford, which currently has a platform barely long enough for a 4 car 350. While there is ample spare land around the station there's a reason why the proposed platform extensions and new large car park would have costed a lot more than Alliance had hoped - subsidence from salt mining in the area.
There isn't a 'one solution fits all' with other franchises - Southern have a mix of 3 and 4 car EMUs (and will soon have 5 car EMUs), LM have a mix of 3 and 4 car EMUs, as do Scotrail, while SWT have a wide variety of different length trains and services. Yet some people seem keen on the idea of Northern getting 319s and losing their 323s and say in defence 'the South works to a 4 car railway so the North can change to a 4 car railway' when the South doesn't operate to a 4 car railway in a lot of cases.
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From what I saw, are 4-car 319s really necessary off peak in the NW when a single 150 or 156 are less than half full. Further electrification and 4-car 319s East of the Pennines will not be enough for growth anytime of day.
There are some services Manchester-Bolton and Liverpool-Wigan which need 4 car off-peak currently.
To me your reasoning sounds flawed. You caught some peak and shoulder peak services in Yorkshire and compared them to some of the middle of the day services in the North West. You need to catch services at different times of the day on different days of the week to get an accurate representation of how busy a line is.
Not that long ago a group of people from Bradford were on the 16:17 Manchester-Chester, which loaded around 170 on a 2 car Pacer. One of them commented on it being the busiest train he'd ever been on. Now can you conclude from that the Mid-Cheshire line is busier than Calder Vale or the Wharfedale line? No. If he'd boarded the 09:17 Manchester-Chester he'd have got a 4 car train with around 80 people on (the 2 carriages on the back are in lieu of an ECS move.) Conversely if he'd boarded the 07:17 Manchester-Chester he would have got around 280 on a 2 car 150, which is probably the most overcrowded train Northern run and not a typical loading for a Northern service in the area. However, possibly the person in question is used to getting a emptyish 333 from Bradford.