Hundreds of thousands of ATMs need hardware (the new currency notes are different in size so the existing dispensers need to be replaced) and software (to dispense only fixed quantities of new notes). The latter is being programmed literally on the fly, and is quite buggy.
Meanwhile politicians and others who've been sitting on huge piles of money are getting it 'washed'/converted into legal money through a mind boggling array of creative schemes. The people who are suffering are those with 'normal' cash flows, from salaries etc, on which taxes have already been paid.
This may or may not have been a good idea in the abstract, but the implementation is a huge huge mess. [1] Public anger is beginning to rise [2], and many black jokes are going around that have the theme, "The Prime Minister made a dramatic announcement, then went to Japan to ride on high speed trains. We citizens are so screwed". This is being applauded by people of Indian origin who don't live in India. As I said above, the idea seems good in the abstract, but the execution is terrible.
Personal Experience: I had to wait 3 hours + in Bangalore to get 35$ worth of small note currency.
[1] From the same source as the OP http://www.firstpost.com/india/rs-500-rs-1000-ban-it-is-the-...
[2] a mainstream newspaper discussing how police is being deployed to protect bankers from the public http://indianexpress.com/article/india/india-news-india/delh...