After enabling FileVault on El Capitan the partition is encrypted in a first pass. After this phase is complete a second optimizing phase is starting which takes considerably longer than the first encryption phase. The optimizing step was not present on the first appearance of FileVault 2 (OS X Lion). The encryption phase took the same amount of time back then. So what is this optimizing all about ?
My system is a mid 2014 MBP with 1 TB SSD. 1st phase was done in about 12 hours. 2nd optimizing phase is now at 20 hours and counting.