API 3.0 is the default API version and we recommend that when building new integrations that you use this version. We will continue to support API 2.0 and 2.1 for the foreseeable future, and will provide at least 12 months notice before switching off those versions.
We learned a lot during the transition from API 1.2 to API 2. This time we’ve made the upgrade much easier to manage. API 3.0 adds new functionality while only modifying existing functionality when absolutely necessary. This means integrators should be able to switch to the new API with a minimum of fuss. It also means that, although we recommend you start to plan your upgrade as soon as possible so that your organization and researchers can benefit from the new features, you have a lot of flexibility in deciding when to update to 3.0.
The small list of potentially breaking changes are in our API release notes here and here. There are a few changes around optional/mandatory fields, JSON enumerations have been modified slightly, and we also have a small refactoring of our XML schemas, adding some new fields to contain the metadata required for the new functionality.