You are comparing slow speed railways with HSR. HSR are substitute to air transport, not the slow-speed railways.
There is a shift. They laid down an advanced system, and are expanding it. Sooner or later it will replace the existing slow speed one, coinciding with the purchasing power of the people. You see it as a substitute to air travel now, may be it is. But what about 5 years from now, 10 years may be. For such a large scale development, such time frames are irrelevant. Just like shinkasen or TGV.
What is the point of finding faults with that system, no matter how you look, Indian railway is doing much worse. For decades it has been just a medium to provide jobs, one of the worst managed system in the world. The only thing to be proud of is that it is probably only system in the world providing such affordable service to a huge number of people. I doubt any other transport company comes close to what IR is doing.