FileVault causing long boot time and terrible lag in the login screen
I have had this exact problem.

I have a 2015 13" MBP running Yosemite (Mac OS X 10.10.5), not Sierra, though I have 8gb RAM and about 20% free space on an aftermarket 500gb SSD (e.g. not Apple factory installed). I use the laptop constantly and travel a lot with it. I've run into this bizarre boot/lag problem with FileVault roughly 2x-3x a year, and as luck would have it, it usually happens when I don't have access to any hands-on tech support besides myself.

The only thing that works for me:


Disable FileVault: boot into Recovery Mode (command-R after startup chime) or if you have another boot partition. I have a TechTool Pro (TTP) emergency boot partition. Run Apple's Disk Utility from that boot partition and use the "Turn Off Encryption" command.
Reset the SMC: shut down computer; hold shift-control-option-power for at least 10 seconds; start up computer.
Once decrypted, run disk utilities on that drive. Besides Apple's Disk Utility for disk and permissions repair, I use TTP's "Volume Rebuild" tool (once I've booted from the emergency partition).
Use the drive for a few days un-encrypted, with several clean reboots.
Boot back into Recovery or emergency partition and run all those utilities again.
Turn FileVault back on.


This typically works for me. However, it's annoying and time-consuming to resolve. And this is a repair, not a fix.  It will still happen again, randomly, sometime in the future.

The fact that you have this problem on Sierra (Mac OS X 10.12) suggests to me that the problem is deeper than just the OS.