Using segwit and creating Pay-To-Witness (P2WPKH) addresses
I might be understanding this incorrectly, but it sounds like the users and/or wallet custodian (coinbase, blockchain.info, etc) must create a P2SH-P2WPKH addresses in order for the witness data to be segregated and save on block space.


Correct, you first have to receive money to a SegWit address. Witness space can only be used when spending outputs received on a SegWit address. The bitcoins can be sent to any type of address from a SegWit input, though.


  Does the new release 0.13.1 default to creating P2WPKH addresses or will the users and online wallet providers have to do this manually? Will there be a built-in RPC function for creating these addresses similar to createmultisig ?


SegWit transactions created before the activation of SegWit could lead to permanent loss of funds, therefore, 0.13.1 will not create SegWit addresses or transactions by default.

→ Please consider the section Upgrade Safety in Bitcoin Core's SegWit Wallet Developer Guide carefully.