1) Relinquish deed: your brother can do a relinquish deed in your favor you don't have to pay stamp duty again.
2)Relinquish deed will be better option as there can be no dispute in future and complete.title will be in your name for time being you can take a POA.
3) You can prepare and register separate agreement with your brother.Stating that you are completely paying the amount for the flat and for time being your brother is coowner as he is supporting you by some help later after so and so time he will execute a relinquish deed in your favour.