Additional loops would help, because some of the single line sections are so long that an intermediate loop would allow the crossing to happen in a different place with less waiting. Dual-tracking as much of the route as practical (several tunnels would be challenging) would be better still, and electrifying as well would be ideal.
I wonder how much of that could have been done for half the cost of dualling the A9, considering that the STPR only recommended partial dualling, at about half the cost, and parallel rail improvements.