It would almost certainly be cheaper for the railway to provide an express service to Exeter via the B&H or Bristol than it would be to spend huge amounts on the WoE line.
Which means in a sane world tickets for the former would be cheaper.
But these days we live in a market without prices, or a command economy without a commander.
The problem is that the B&H and via Bristol routes to provide extra services from London is going to be expensive.
Whilst this also true for the WofE line, in that you'd need something like Crossrail 2, however the paths from London are a by product of Crossrail 2 (in that the costs of Crossrail 2 would be funded by its services rather than the services out of Waterloo).
Given that there's then 8tph, but fairly limited scope for more services South of Basingstoke or Guildford it's then a car if try and fit the services on lines which have the capacity or are cheap to add capacity to.
The Alton line could be a contender, but you'll probably not increase passenger usage by much at 4tph compared to 3tph.
You could run more services turning around at Basingstoke, but with the the potential for the Southern Approach services you don't really want more than 4tph doing that.
That leaves the WofE line, along it you could run services to Southampton and Weymouth. However there's still going to be some portions/services which would be spare with the scope to go to Exeter.
Yes you'd need to do redoubling, but you would need to do that for any increase in frequency.
As such I would be included to do the following:
- 1tph Waterloo Weymouth/Bristol (Clapham Junction, Basingstoke, Andover, Salisbury and then all stations beyond the WofE line)
- 1tph Waterloo Southampton/Exeter (Woking, Basingstoke, Andover, Salisbury and then stopping beyond Salisbury)
- 1tph Waterloo Exeter (Basingstoke, Salisbury, Honiton, Exeter Central, Exeter St David's)
- 1tph Waterloo Southampton/Yeovil (Waterloo, Clapham Junction, Woking, Basingstoke and then stopping)
Doing that should get you, without any line speed improvements, a sub 3 hour London to Exeter service. Although not enough to bet a Paddington service; it should be enough to get to Exeter from Basingstoke quicker.
It would also likely be the quickest service from Waterloo to Basingstoke, attracting some passengers on to it from other services.