Like every other film industry, Bollywood movies also have a indie counterpart. I've seen quite a few, though it might not translate very well to a watcher who is not familiar with the cultural context for the movies.

Still if you want a list of movies which are "serious" but still approachable enough (i.e doesn't gaze at it's own asshole) and fairly new, I do have a few recommendations -

Udaan, Kahaani, Satya, Maqbool, Khosla's Nest, Masaan, Detective Byomkesh Bakshy, Gangs of Wasseypur, Johhny Gaddar, Kaminey, Black Friday (2004), Aaranya Kaandam (not bollywood)

This list isn't some exhaustive "greatest" ever, just some oddball movies which stick out in my head.

Also keep it in mind this is just the list of Hindi/Bollywood movies which were historically known as "Indian" movies. Other regions of the country have their own list of favorites.