The overhaul of the terminal interface will probably cause a range of minor issues for existing users. This is inevitable for such a significant change, and we’ve done our best to minimise these issues.

It goes on to make suggestions for handling changes.

IPython also introduces the following backwards incompatible changes:

• The %install_ext magic function, deprecated since 4.0, has now been deleted. You can distribute and install extensions as packages on PyPI.
• Callbacks registered while an event is being handled will now only be called for subsequent events; previously they could be called for the current event. Similarly, callbacks removed while handling an event will always get that event. 
• Integration with pydb has been removed since pydb development has been stopped since 2012, and pydb is not installable from PyPI.
• The autoedit_syntax option, which has apparently been broken for many years, has been removed

One reason for IPython 5.x having long term support, with fixes for critical bugs by the core team until the end of 2017 and beyond that in response to pull requests, is that it is the last major version to support Python 2.  IPython 6.x will require Python 3.

With regard to this decision Matthias Bussonnier writes:

If you are a Python 2 user, be reassured, we will make sure that upgrading does not unexpectedly install IPython 6.x and break your system. You can decide to stay for a longer period of time on IPython 5.x LTS and decide to leapfrog a few IPython versions once you migrate to Python 3, though we recommend keeping up to date with the latest stable versions as they are released, and of course to migrate to Python 3 when possible.

IPython is the first IPython/Jupyter project to drop support for Python 2, but you can expect other components of IPython/Jupyter to follow. Since its inception, JupyterHub for example as always been Python 3 only.

It is important to note that users will always be able to use a Python 2 kernel with the Jupyter Notebook, even when all of our projects have transitioned to Python 3: as part of our LTS commitment, we will make any necessary updates to the IPython kernel so it can continue to work in a Jupyter Notebook for the duration of our LTS support.

He also notes that IPython has signed the  which is a pledge to drop support for Python 2.7 no later than 2020 to coincide with the Python development team's own target for ceasing support for the Python 2.x branch.