1) There are not many instances, just a couple of particles, some pickups, the player and some simple platforms for level creation. Screenshot below. 2) This is in Unity on a pretty decent iMac. On low end mobile devices this seems to cause a bottleneck that can take up to 6-8 seconds of black screen.
Well seeing Playmaker in your Hierarchy, I would venture to guess that the FSM is taking up a good portion of the initialization time. It all comes down to what your scripts and objects are on each Object you're initializing. It all adds up.
You can try setting some of your pool items to 0 instances to compare time and narrow it down to which prefabs are "heavy".