London, Manchester, Newcastle etc don't? I don't buy it.
Of course, no one likes losing their job. I think if London tube drivers are going to kick up an almighty stink about later shifts, then Liverpool guards are going to naturally not be at all chuffed losing their jobs, which is much worse. It's natural, though, unlike the tube drivers with respect to London, if it does kick off, the media and various individuals on sites such as this will no doubt no miss the opportunity to pounce on it as an opportunity for confirmation bias - "Scousers, eh?" etc etc.
Anyway, if played correctly, redundancies could be cut much further. Expansions to the system (i.e. Skelmersdale link which is a no brainer to me), increase in frequencies on certain services (as you touch upon) and at least slightly later operating times, at least on weekends (although that latter one is controversial in itself if London is anything to go by). Most of these things can't be achieved currently due to the limited amount of rolling stock. More later services could but it's more everyday wear and tear on what is rather elderly rolling stock. Probably won't get such joined up thinking though.
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If it has to be a choice between 6-car trainsets or higher frequencies, I'll choose the latter. Clockface 4tph on most branches is good but 6tph is much better and once it gets to that sort of frequency, people stop caring about the timetables and just turn up at the station whenever. My bugbear with mixed formations is that people often end up waiting at the wrong end of the platform and in busy periods then bunch up in the nearest car. It doesn't help that the new destination boards make no mention of the length of the train. Platform doors or gates with numbers on them could help. Even just pavement markings would.
Like I said, some services can be quiet on weekday nights. I used to frequently do Central-Cressington at evening rush hour and make the return journey around 9ish. The outbound train would be crammed, so much so that it was uncomfortable, whilst the return would only have a few people on it. I reckon for a lot of people, the frequent 82 bus is seen more favourably at that time of night as they're much more than every 15 minutes and traffic on the road is light at that time. I suppose with fixed formation the question is: how much more expensive is a 6-car train to run compared to a 3-car one?
We could, of course, go for some halfway fixed formation, as Neil suggests, but as a fixed formation, this reduces the maximum overall capacity of the network. I'm thinking of the scenes of chaos that you see in the underground stations when there's a big event on in the city, even with 6-car formations. That said, with more actual trainsets, it may be possible to compensate with a high frequency. I believe the current capacity in the underground sections is much higher than what's currently used.