@Iron117Prime Belated Welcome to the forums c:
I'm sort of skeptical of seeing Aku anywhere other than the Samurai Jack side story. Main reason being due to Jack's current attitude. If Jack knew that Aku was still alive, would he be wasting time as a teacher? Would he not be actively hunting him down, as he did in the show?
A while back, BeeAre shared a little info with us. He said that the Time Squad didn't exist in GT's timeline/universe. I believe that the reason for this is due to Aku not allowing anyone else the ability to time travel. If he were still alive, I don't think he would have allowed the Time Squad to have formed in PPGD.
It's true that Aku has been confirmed to make an appearance, and it's been mentioned that Dr. X and Jack will have some sort of connection. It's also been confirmed that the two universes/timelines split as a result of Jack making some decision in the past (if I'm remembering it right, it's something that we have not seen yet). One of the popular theories about this decision revolves around whether or not Jack kills Aku in the past. If Jack kills Aku, then the PPGD universe/timeline comes to fruition. On the other hand, if Jack shows Aku mercy, then that leads to the GT universe/timeline. When you take into account Dr. X's involvement, though, it's possible that something else may have occured.
It's been theorized that he could be from the same future that Jack was sent to in the show. In which case, it's possible that the decision that Jack makes revolves around accepting Dr. X's help. If he does, then they both go to the past to defeat Aku (and somehow make it to present day Megaville in PPGD). If he doesn't, then he fails in his mission to kill Aku (which in turn leads to GT).
"A reader lives a thousand lives, the man who never reads lives only one." - George R.R. Martin