Some of the things you mentioned in deficiencies.
1. 65kmph avg is not low. It is KR and single line. There will be crossing.
2. CC is not normal CC which you see in shatabdi, it has foldable legrest, which means you can relax very well
3. For people going to Goa, Karmali is closer than MAO. Karmali is in the heart of goa.(but...
more... am not sure about connectivity from station, but i guess, with this train, it will increase for sure)
4. 5AM is not too early. It is just early departure, and this train is mainly for tourist, and they wont mind going early
5. Fare is not at all high, just do a reality check about food price.
6. Flight prices are dynamic and will increase rapidly, and the view KR provides can never be given by a flight.