This interesting bit from the reddit AMA:
We had other story debt we needed to pay off this season, and a limited number of episodes in which to do it. We kept him around as long as we could justify to tie up his arc from PoF, but we couldn’t make him the main threat this season.
If Joko wasn't supposed to be the main villain of Season 4, then are we gonna meet them in the next episode? Will there be enough episodes to flesh out a new awesome villain? Because we are already on Episode 3 of Season 4 and a main villain needs to be well designed. From all the characters we've seen in Season 4 so far I can't say I can pick one out as the potential main villain, so it's either gonna be a new character, or an old one that comes back and/or betrays us.