Welcome to the Phase II forums. That is a hard question to answer. By the time I came to Phase II, I had become a Star Trek Fan Film Fan, driven, as perhaps you are, by J.J. Trek, which I took as the Death Of Pro Trek. Therefore, I watched this series from the pilot, which is not a great fan film. However, World Enough and Time, and Blood and Fire parts 1 and 2 are, IMHO, among the top 5 Star Trek Fan Films of all time, with WE&T IMHO, being No. 1.
Having seen JJA Trek, you are already familiar with what started at Phase II... recasting the original series characters. If you promise yourself you'll watch them all, the advantage of starting with the Pilot is that you will be used to the new crew by the time they hit their stride, and you won't be stopping as asking yourself... was that Scotty? Am I supposed to know who that was? I can assure you, speaking as STRICTLY A VIEWER they are worth watching.