I travel by train with bike frequently, with a bit of planning and avoiding the busy times I've never had a problem. If booked well in advance it's also cheap. When I did the E2E in 2005, Derby to Wick cost £28 and Penzance to Derby £22.
The Bristol to Edinburgh route has recently changed hands from Virgin to Cross Country. The pricing policy has changed, it looks like it's going to be easier to get a cheap ticket, but there's not going to be the few super bargains that there were. It's too early to tell if it makes any other long term difference.
In the peak season Scotrail transport bikes by van from Inverness to Thurso/Wick, well they have for at least the last three years. It's very secure, you load your bike and the van gets there before you and waits. You have to make a bike reservation with Scotrail, they won't let you on without. That should be easy enough, except my local station keeps telling me it isn't necessary, their computer system can't make the reservation so they assume it's not needed! I've printed out Scotrails terms and conditions and take this along, I still have to insist they ring them up and make the reservation.
There's also a coach that goes to Wick that takes bikes. I'm not sure of the details, I met a couple in a Wick B&B that had just come up on it. It took longer but they said it was an enjoyable trip.