Frames per seconds is better in almost every way. When you use it to watch movies it is better since a normal human understands seconds but not what a frame is. In gaming, frame times usually vary quite a lot, and the average, which is fps, is the important part.
When doing real-time graphics and looking at a profiler, it does help to know that you want to have less than 16 ms of calculations per frame. But agreed, in most other respects fps is nicer.
