Let’s start at the end: Is Ahsoka alive? Yes. Until she isn’t. I’m sure she will return, but she will be very different. Having your worst fear confirmed will do that to you.
It turns out that Maul still ain’t dead. Yet. I have mixed feelings about his post-The Phantom Menace storyline, but I won’t discuss them now. There has to be a definitive resolution to Maul’s character arc at some point; the fandom deserves it. I don’t want him popping up in anything that takes place between Return of the Jedi and The Force Awakens.
The Fifth Brother and Seventh Sister went out with more of a whimper than a bang. That’s fine, since they really didn’t have all that much to do this season. When the Eighth Brother showed up, I thought he was being set up to be the big bad for season three, but no. He went away as fast as he arrived. I think the Inquisitors have run their course.
The next big question to ponder is whether or not Ezra will turn to the Dark Side. It’s hard to say if it will make for a better story. I just don’t want Rebels to drag out the will he/won’t he thing forever.
The inclusion of Darth Vader in season two could have been a gimmick, but it wasn’t. What made it work was his confrontation with Anakin Skywalker’s former apprentice, Ahsoka Tano. This something the fans have wanted since the end of The Clone Wars, but thought they may never see. I don’t think “Twilight of the Apprentice” disappointed even the most skeptical Star Wars fan.