1. Population - We have too many people, but a very small percentage of that contribute to the country by means of paying tax. It's a liability, both in lower and higher levels. We have too many mouths to feed but not so many bread earners as we would like it to be.
2. Sanitation - So many people, it's a burden over the infrastructure. Social awareness is also pretty low.
3. Lack of education - Lack of basic education in some levels as well as higher education. Our premier institutes have become glorified schools for churning out skilled workers, following the demand-supply curve.
4. Imbalance in industry - We have too many people working in the Service sector in comparison to the others. What will happen when the bubble bursts ?
5. Lack of democracy - Yes, we are the largest democracy in the World and we are lacking in that front - lack of proper representation of the people. We have loyalty voting, paid voting, religious vote banks (rigging has been handled well by the EC). We also have sheer lack of interest, when it comes to be a part of democratic process - mostly in the middle class section. Hope that will change gradually.
6. Uneven development - The maoist insurgency issues or some other similar issues in the North East could have been easily handled had there been proper and evenly distributed development in those areas. No matter how much nationalistic we are, people need basic amenities for life and support from government, that's his right. If development is uneven, then people will have grievances and there will be other kind of people who will try to exploit those grievances to channelise it towards destructive ways. Our priority should be to treat the cause first and then the effect.
I can think of 6 as of now...Will add a few more if anything crosses my mind.