I often hear horror stories like this, but in my three years of regular train travel, not once has anything bad happened! I always book well in advance and have a reserved seat. My trains have been early a few times, but never late. I know I sound like a PR person for Great Western, but honestly I am a huge booster. I love the train!
Being a student (even with a railcard), I can't afford the luxury of booking in advance or reserving seats - but although I do usually manage to get a seat, I am prepared to stand because the trains are busy and sometimes it happens that there are no seats available. With a ticket bought on the day (i.e. a saver return), I'm not paying an extortionate amount, so I don't mind that much.
Once, on a train from London Paddington to Exeter, I had to stand for more than 2 hours - and ended up reading a whole book while I was there! On that occasion, I'd paid for a reserved seat, but two old ladies got on the train and one took the seat opposite me - I couldn't let the other one stand for 2 hours, so I switched with her and stood instead.