The biggest shake up would appear to be the non-refundability of advance purchase fares if plans change. With travel times up in the air a lot of the time due to the weather, track and signal failures within the railway system, not to mention external failures and necessary changes to one's itinerary, it is clear that the changes will probably favor the train operators.
The plan, of course, is always to maximum the revenue per seat (and, unfortunately per aisle space as well) so that the profits can be re-invested in a better service.
Sadly I have just about given up on rail travel in recent months. It's all about reliability, or the lack of it. Higher prices won't help to bring me back.