Matt,
Did you install a Subclipse or Subversive plugin to MyEclipse for SVN client support? Is the plugin version same as in MyEclipse 2014 ?
MyEclipse 2015 is based on Eclipse Luna whereas MyEclipse 2014 is based on Eclipse Kepler.
It might be possible that the Merge functionality differs basing on the SVN and the Eclipse version.
If possible, please install the plugin to Eclipse Luna 4.4 and check if it works as expected.
Please send us the exact steps you followed to install the plugin along with a screenshot of the Merge wizard for further investigation if the plugin works as expected in Eclipse Luna.
–Swapna
MyEclipse Support