Way back in October 2010 we released JIRA 4.2 and the first real REST API for JIRA. We continued to add to it over 4.3 and 4.4. By February 2012 we felt confident in the direction our REST API was going and removed the alpha and beta labels from it in JIRA 5.0. The scope of the API continued to expand over subsequent releases: 5.1, 5.2, and now 6.0. With the continued growth of our REST APIs, we made the decision to officially deprecate the SOAP and XML-RPC remote APIs in JIRA 6.0.
Deprecating SOAP and XML-RPC means that developers have a clear and consistent message from us about how they should be interacting with JIRA remotely. They won't build up code relying on SOAP and then be disappointed when new features don't get added or bugs don't get fixed. No false hope and no bullshit: REST is the future.
Of course, we know that there is a lot of existing code out there so we're not going to remove SOAP immediately. Our intention is to remove SOAP from JIRA in release 7.0.
SOAP and XML-RPC will continue to work without change during the JIRA 6.x, however we won't be spending any more effort on bugfixing or feature requests. When JIRA 7.0 is released the code will be removed from JIRA and they will become unsupported by Atlassian.
Right now the JIRA REST API has pretty good coverage of the SOAP API but it isn't 100% complete (we are at around 90% at the time this article is updated). Atlassian is absolutely committed to making every feature of the SOAP API available in the REST API. Making that happen is a precondition of removing the SOAP and XML-RPC APIs from JIRA. We will be working toward that goal during the 6.x development cycles.
For more details, see the JIRA SOAP to REST Migration Guide.