Delay in registration of Apartment deed by Builder

Q: I purchased a house in Wagholi, Pune in Oct 2011 (date of registration of the house) and got the possession in Jan 2012. All formalities, payments & documentation were completed before possession except the deed of apartment, which the builder (& broker) said will be done soon. After much persuasion, the said deed was given to us by the builder in July 2013. Now, in order to get the apartment deed registered, the builder is asking us to pay the change in stamp duty which taken place since the time we bought the house (stamp duty has changed from 2% to 5% since). My qs is why should we pay for the fault of the builder? the onus of the delay completely lies on the builder. What is the way out?