Any direct line between Exeter and Plymouth would most sensibly follow the route of the A38 road skirting Dartmoor rather than burrowing under it! Torbay could be served by using the Heathfield branch to Newton Abbot. Nevertheless it would require some hefty engineering features including a 2 mile tunnel under Haldon Hill (which is greensand rather than granite) and a high-level bridge over the River Dart at Buckfastleigh. This is fantasy stuff and won't happen any time soon - re-opening the LSW line via Okehampton is a much more realistic and achievable option,and at least provides an emergency diversion. The Teign Valley line is a complete non-starter, being lightly constructed and steeply graded whilst the formation is obliterated by the A38 at Chudleigh Knighton and the A30 at Alphington.
It has been demonstrated that tunnelling is often the cheaper and easier option than a longer diversion.
The lowest capital cost option for HS2 would involve almost no tunnels outside the M25 at all.
But this was deemed to be a non starter.
Whilst tunnelling appears to be expensive it is nowhere near as expensive as it once was compared to surface operations (tunnelling is now only a small integer times as expensive as surface running compared to orders of magnitude as was in earlier eras).
There are no NIMBYs complaining about their view when the line is a hundred metres or more below Dartmoor.
It's not just air though, the traffic statisics for the A38 show a significant drop in traffic after Exeter even though there is no change in the speed limit. Even if you improved rail journey times to Plymouth, Exeter is always going to be the first city people arrive at and Pymouth doesn't have anything more to offer.
Plymouth has land.
Land is the most important thing of all.
Housing in Plymouth would likely be cheaper than in Exeter for this very reason.
If a high speed route allows my proposed non stop running Plymouth station would be something like 55-60km further from London.
This sounds like a lot but it translates to
twelve minutes.