Ever since I started to play/work with any Arduino about a year and a half ago, I have exclusively used the 1.5.x range of IDE and never had any issue one any of the boards I have written scripts for (and by now, I have used all the existing variations of Arduinos)...
If you are using a Yun (or Due), there is no need IMHO to use any of the older IDE versions. Using the Intel Galileo is the sole exception here, and the presence and use of that specific IDE (1.5.3 as available from Intel's web site) has never interfered with any of the stuff I did so far for the Yun or any other Arduino...
Ralf