Simple problem - people. People are idiots, particularly in packs. No-one wants to be that one person who doesn't get onto a train.
I've heard guards/station staff announcing repeatedly that there is a train following just moments behind that is mostly empty, yet people will still try and cram onto this train to save a couple of minutes. Yet of course if they had allowed the busy train to leave and waited for the next train they would probably have arrived at the same time.
These are the same people who stand in the middle of a platform and crowd onto the packed middle coach, then stand in the vestibules. They are everyone, they are no-one, they are the mob. No amount of announcements or signage will change their behaviour.
These are the people who insist on catching the same train every day, even though they know it will be crammed and complain every day. Rather than accepting it will be busy and going slightly earlier into town, or waiting in town longer before coming home (yes I know not everyone can do that, due to childcare etc. but I'm sure many people could take a slower walk to the station in the evening to get a later, quieter train, for a more comfortable journey. I did for 2 years when I worked in Leeds and it was well worth a 30 minute later home arrival for a seat and relaxed journey).
Careful timetabling will help, but there are only so many trains and paths available and skipping stops is only of benefit to those who start their trip furthest out. Unfortunately the only real way to resolve this issue is with live platform and train management - literally allowing only a certain number of people onto each train at each station (like those motorway junctions with traffic lights). Stopping quieter fast trains at smaller stations reactively if there is a large passenger build-up (afterall, if the slow trains become overcrowded they have slow dispatching and this will hold up fast trains anyway). However, this will require big infrastructure and operational changes and obviously for everyone who lives closer to the city who can now get on a train, someone further out is going to miss theirs.