Part of the reason why the best students used to go abroad was because there were a lot more job opportunities in the US after a graduate degree. This is changing now with MSR India, Intel Research India, GE Research, TCS Research and so on becoming well-established labs in their own right. The job scenario for academic jobs in India is way better than it is in the US and a moderately competent candidate can easily get jobs now at an IIT/IISER/ISI.
As someone who is keenly following higher education in India, I think the state of higher education is better than ever and rapidly improving. An easy way of judging this is to look at where our students are ending up. The best undergrads in India today invariably end up at the best schools in the world. This wasn't true 30 years and there are many examples of really high quality IIT graduates who studied in mid-tier US schools. Even students from second-tier schools like, say CEG Guindy or NIT Surathkul, now end up at very very good universities. The situation is less good in the humanities and social sciences, which btw are struggling the world over, but some of the newer IITs have social science and humanities departments and some progress is being made [1].
[1] http://nanopolitan.blogspot.com/2013/01/sukhdeo-thorat-on-so...