There are the following things which need to be taken care of:
1) The soap API includes a few things which are not available in the REST API, most prominently describe the layout, queryAll, getDeleted and getUpdated.
2) You can directly update bulk data in the SOAP API, but you'll need to use the Async Bulk API to do that from REST.
3) The REST API can access binary data (files, attachments, content, etc) without the overhead of base64 encoding/decoding.
4) The REST API contains a few things not available in the SOAP API, which includes the API for chatter, and accesses to the recently accessed records lists.
So, depending on exactly what your app is trying to do may push you one way or the other.