As you know, the Bangalore-Pune route was on MG and the Pune-Bombay route was on BG. So, an end-to-end train between Bombay and Bangalore via Pune and Hubli was not possible before 1995.
If you mean, why not they have a BG train on the Pune-Bombay section that acted as the BG portion of a combined BG-MG mail service from Bangalore, then it was because the amount of traffic was far lesser in those days and the British method of operations was also quite different. However, there were connecting BG...
more... trains to Bombay from Pune, and 1st class passengers could book a combined ticket from Bombay to Bangalore.
Like I said, until 1983, there was no BG route from Bangalore to Bombay. The only route was via JTJ-RU-GTL-Wadi. In 1983, the SBC-GTL section was converted to BG and for the first time in history, it was possible to run a direct train between the 2 cities. In 1995, the SBC-Miraj section was also converted to BG, which gave another direct route between the 2 cities.
Also, Bombay was already more important than Pune by the time railways started in India in 1853. It was the Brits' main centre on the west coast. In fact, Bombay, Madras, Calcutta and Lahore were by far, the largest and most prominent cities in the British territory between 1850 and 1947. All the other cities, except Delhi, were far, far behind these 4 cities in terms of importance.