Apple is launching the iPhone SE on 8th of April in India for Rs.39,000 for the base 16gb model. The iPhone 7 is due to announced around September 2016 so a price drop for the iPhone 6s will be coming in a few weeks or so.
This means the iPhone 6s will become cheaper than the iPhone SE. The iPhone 6s has slightly better specs than the iPhone SE and now retails for Rs.41,000 to Rs.40,000 without any offers; so holding off the iPhone SE for the iPhone 6s is a better option has you are even getting the 3D touch on the 6s. The only downside is that people looking for the smaller form factor iPhone will have to pay more for a phone which is a mix between the old and new.
Going for the iPhone 6s rather than the SE is a better option (in India at least) as you are getting better hardware and internals for your money.