2 main challenges.
1. The distance is fairly long for a Vande Bharat Express. The distance between Mumbai and Mangalore is nearly 900 KMS, whereas the longest VB runs for 760 KM with an avg speed of 95 KMPH
2....
more... KR will still be a single line after electrification and entire route doubling will take minimum 10 years considering the time for sourcing funds, getting all approvals, construction time, track realignment, station re-modelling etc.
Further KR has an MPS of 120 KMPH (though this could be improved upto 160 KMPH in the non monsoon timings). IR would be much better off running an overnight train between these sector. People who want to travel fast will definitely prefer flights.