Just in case anyone is interested in knowing more about X-Plane certified.
The only significant software difference between the certified version and the desktop version is that because the certified version went through the certification process and because of that it will not undergo any regular updates as it would need to be certified again. That means that the game version is more up to date with more features than the certified version. Without checking I believe the certified version is X-Plane 7.x and the game is version 9, so there are significant upgrades in the game version. So with that in mind unless you need a certified device ($100K plus) for training that will get you credits against your hours, stick with the game.
Just so that I do not get called out, I should add as a point of clarity that the software is not certified, it is the whole flight training device (including the software)