660cc Jimny is turbo charged which 1000cc equivalent
Fuel Economy almost same for both, 660cc slightly better
Probably you can get 1300cc Jimny, mostly 1999-2002 models. Which is quite old compare to 660cc where you can get latest models with price around 12lac.
1300cc slightly better in terms of power(Depend on engine condition)
I will suggest go for 660cc jimny which better value for the money, you will get latest model with same price.