Disney had Clone Wars wind down so it could start up Rebels, probably not wanting to make the same mistake Star Trek did in the 90s of having multiple series from the same franchise on at the same time (a lot of fans divided between shows, hurting each's ratings, as well as the glut of Star Trek causing a degree of franchise fatigue). While I'd have been happy to see more Clone Wars too, I think they were smart to end it largely when they did - Ahsoka leaving at the end of season 5 felt like a great closing point for the series, and the "Lost Episodes" on Netflix are more of a nice bonus than truly necessary.
I also don't see that they short-changed Maul in the slightest - he had 5 out of 20 episodes of season 5, including a number devoted solely to him and Savage as the main characters of those episodes (no Jedi or clones even show up in some), and he has a major arc throughout Rebels. What does it matter if his story is told in one show or two? At this point he's arguably the best developed Star Wars villain outside of Palpatine and Vader, and is easily on par with Dooku or Ventress in that regard.