What adds the limitation to the throughput of S2 series modules?
The bandwidth of XBee is 250 kbps as per specifications but during the tests with S2B modules we are only getting the throughput of 20 kbps.
Which module/layer adds to the delays, is there a way we can overcome this?
You are getting confused between the fixed RF data rate and actual throughput cable after the RF protocol is included.
The networking layers add a great deal of the over head.
No, there is no way to reduce the over head on this protocol.