Conspiracy theory: Railway Board has taken upon itself to destroy IR.
Flexi fare is a scheme meant to destroy railways and let the aviation sector win more easily. The premium trains are the sector which are competing with airways and a price rise there will mean a win for aviation. Shatabdi are day class trains and seats fill at the last time, by rising fares, they literally made them empty. Durontos are a failed concept on many routes and couldn't take the price hike.Even Mumbai Raj couldn't fill all seats on few days.
"Tickets...
more...

under current booking shall be sold at the last price sold for that class and other supplementary charges like reservation fee, superfast charges." If seats are not filled until the last minute, what makes more sense, selling them at the original price or the higher price.
Flexi fare increases fare from the start and caps it at 1.5x when 50% of the seats are reserved, thus leaving the rest 50% of the seats doomed[few purchase them at the high price]. Think why IR didn't start dynamic fare principle on these trains where price is set via demand. In that case, if a train is not getting pax, the fare will automatically be lowered and attract passengers. Think why IR didn't increase fares of those trains that are in constant demand. Many non-Raj trains remain in super demand all through the year and a small price rise there wouldn't have done anything. If IR is so hard pressed for revenues, why aren't they increasing suburban rates where literally there is no competition. And ultimately, why are they still running so many loss making trains.
From what I see, either the RB is full of stupid people who literally have no idea what they are doing or they are in bed with the aviation industry and are willingly destroying the railways. I can't see any other reason for their rash decisions.
Call me foolish or paranoid but I see no other reason as to why RB is doing such things.