Instantiate, Transform.parent and GameObject.SetActive all take longer than they used to in Unity 5.3.

Reproduction Steps:
1. Open the reproduction project in "case_786605-InstantiationTest.zip" in 5.3
2. Run the scene MainScene
3. Attach the Unity Profiler to the Editor
4. Press any key to run the behavior in the CubeInstantiator script
5. Note down the values in the Profiler for the custom markers
6. Repeats steps 1-5 in version 5.4
7. Compare the two sets of values, notice that 5.4 is worse

Note that these numbers are slightly better in a build, rather than in-Editor, but a performance regression still exists.