I suppose I'm content with this list. Not what I'd have said, honestly, but no major complaints here.
For me, I would have chosen 'No Country for Old Men', 'Fargo', 'Inside Llewyn Davis', 'The Big Lebowski', and 'Miller's Crossing' for my top five.
Some of these are terrifying (i.e. the second one!) but, as you said, this just shows the the spirit of indie filmmakers who don't necessarily have the financial capacities of more professional filmmaking teams.
Cinematography: 2001: A Space Odyssey (Geoffrey Unsworth), Gravity (Emmanuel Lubezki), Barry Lyndon (John Alcott), Three Colours trilogy (Klosinski, Idziak, Sobocinski), Stalker (Alexander Knyazhinsky)
Directing: Citizen Kane (Orson Welles), Tokyo Story (Yasujiro Ozu), 8 1/2 (Federico Fellini), The Searchers (John Ford), Goodfellas (Martin Scorsese) Andrei Rublev (Andrei Tarkovsky)
Story: Chinatown (Robert Towne), Pulp Fiction (Quentin Tarantino and Roger Avary), Casablanca (Julius J. & Philip G. Epstein and Howard Koch), Network (Paddy Chayefsky), All the President's Men (William Goldman)