Yes thats a very narrow view but look at the complete picture.
Infra investments, kind of crowd... i think what we have in India is best for people in india. If you want high speed train, it comes at premium price. India main problem is capita per person which is very low. Also, indian railway is designed for volumes and thats because of population. In Europe or Japan (have been to both countries), you have hardly any train which has more than 8 coaches and each coach is around 40-45 people in different config. In India if you run railways like this, there will be no ROI. So perspective, condition is different.
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to it the budget is distributed and focused on 18 zones - here comes the size of country. All european countries (except France) incldg Japan, the area to cater is very less and route allocation in India is politically driven. For examples some of the train should not be even running in IR network, but they are because of vote bank and what not. Same goes for stoppages. Here in EU countries all the main cities are connected with train with almost a stop in between which will be an important city. All metro train then provides connectivity within city. These metro trains connect from Hauptbanhof (central station) in cities to all places. Eg. Paris - Amsterdam Thalys (clocking a speed of 350kmph +) originates from Paris Nord and halt only at Brussels Zuid, Schipol Airport (Amsterdam) and then Amsterdam Centraal.
If you want to summarize, you are comparing railways in a developed country with a developing country.