The IITs are quite solid and several are among the pool of top institutions in the world. There are many really good engineers and scientists in the country.
More interestingly, the upper bureaucracy (i.e. non-political appointees) of science and engineering oriented ministries (e.g. MNRE) tend to be actual scientists.
There's a pseudoscientific froth in India, Turkey, USA, Iran, and other religious countries, but they still get power plants and satellites built. The froth gets attention because 1> it's shocking and 2> it appeals to the short-term aims of various politicians and their bases.
So when India can't get a fighter plane built I ascribe it to garden variety corruption, not disdain for science.