The same project ,on same android device. Use Unity 5.2.4 builded app load my scene use < 2s , but use unity 5.3.3 builded use time >3s. Unity 5.3.3 is load slower than 5.2.4 very obvious.
Attach the screenshot from Unity 5.3.3p1 builded package:
Yes the performance of Unity 5.3 is much worse than 5.2x for sure and discussed in a lengthy thread. Try and post a bug report maybe they work on some performance stuff.