A someone who is/was a rail commuter, and also someone with an interest in the rail industry, I thought I would throw my tuppence in this discussion for a change.
I would summerise the issue in that the "off peak is the new peak".
I have observed that trains are generally quiet until 9.30 - at which point they are getting busier (and more so each week). I used to be in the office for 8 every day, I now work from home a couple of hours, and catch the first offpeak trains whenever I can - its cheaper to do this than an 8 in 28 ticket which is priced between the Anytime day, and Off peak day return (and feels like a rip off to me, and many others - and also commented on by quite a few in the article).
Surely this just boils down to Supply/Demand. Demand is there before 9.30, but the price of anytime tickets mean is prohibitive for all but those who need to travel at that time (which is now, hardly anyone). The easy answer is to get rid of the Anytime fares and make the CDR/SVR valid all day - not sure who's going to pay for it though.
I have also noticed that people who have a car, and now choosing to drive all the way, rather than park and use the train. Could removing parking fee's from some stations help make the train more attractive again? Take Retford to Sheffield commuter, It would cost £10 to park at Retford for the day, plus the train fare. It would cost my £7 to park in Sheffield city centre for 10 hours (or £4.50 at a park and ride site near by), plus around £5 for petrol, including a bit for wear and tear. All things considered, if you have a car, its probably cheaper to drive (London excluded) - and thats before you start comparing a door to door drive, or every 10 minutes park and ride service with the hourly northern service on that route.