I have been experiencing a very similar issue since I install Sierra on my 2015 13" MBP. It occurs whether standalone or on my docking station with Monitor, Bluetooth keyboard/track-pad, and external drives connected.
Description of issue:
1. If the laptop has been shutdown or in extended "Sleep" (6 hrs +), upon startup or "awaking, it will go to the login screen and freeze for 5 minutes or so until the login box appears and is accessible. When attempting to enter password, it will freeze again with initially the spinning ball which then itself freezes. Again after several minutes, the box becomes active and password can be entered and accepted.
2. It will take 3-4 minutes for home screen to fully appear and become accessible. Initially, only the bottom of the screen with the menu bar is loaded, but is not functional (no response to selecting). Once the full screen is loaded, the system is usually fully accessible and functional, although on occasion, it will become very sluggish and temporarily freeze.
3. At times this process fails and I have to use power button to shutdown and start the process again. This is repeatable over multiple attempts and days. I reinstalled Sierra with no change in the issue
This is beyond annoying!