HI Aditya,
As Christian Libich rightly pointed out SAP RFC calls are SAP native web service methods and in addition to his points, SAP JCO RFC calls also support
- Single sign-on
- Crucial cross module validations required for a transaction execution (Eg., Material lock check on Goods movement, Order status check on Creating Time Ticket etc..)
- Message Queuing for exactly once in order execution of a set of RFCs & Data buffering for the queue job.
So with SAP MII as your front end tool for data retrieval and execution, it is recommended and is always better to go with SAP JCO based RFC calls.
With regards,
Ponilango