While both are flawed saga's, Johto earns my vote for numerous reasons. While I agree that Johto had too many fillers and Ash's Johto team was underdeveloped, there's just so much reason why I like Johto over Unova. Here's just a list of the reasons why I prefer Johto over the train wreck that is Unova
1. The cast: The original group of Ash, Brock, and Misty will always be a favorite of mine, mainly because of the chemistry that there was between them. While BW had some interesting chemistry, Iris to me was very unlikable and her continuous "You're such a kid!" comment was just annoying and unlike how Ash and Misty would argue, this was ignored by Ash mostly. Misty and Brock, while you didn't get as much focus as you deserved, you will always be the best traveling companions for Ash.
2. The episodes: While there were several filler episodes, I found them a lot more enjoyable than the ones BW had, mostly because I did like the humor in them a lot more. Plus the COtD's weren't as bad as the ones in BW, most of which were either bland or had stupid gimmicks and quirks.
3. Team Rocket: While they have gone back to their old ways and have even began using their original motto again, they were a lot more enjoyable in Johto thanks to the slapstick humor and jokes. They're far too serious in BW and their scenes where they're conniving/spying on the twerps aren't as fun in BW.
4. The gym battles: Ash had made a big improvement since Kanto and in Johto, his gym battles were more fun to watch and he actually got badges by beating the gym leader. There was a little more strategy and less OHKO's in Johto than in Unova's boring battles.
5. His team: While Ash's Johto team was underdeveloped and got shafted often for his Kanto team, I liked it a lot more than the expansive team he had in BW.
6. THE LEAGUE!!!: The league was hands down far better than BW's horrendous league. Not only was it longer, but Ash got 5 on screen battles(Salvatore, Macy, Jackson, Gary, and Harrison) that were actually very fun to watch, including the long awaited 6 on 6 with Gary(Unlike in BW, Ash only got a 1 on 1 with his main rival Trip) It was also one of the few leagues where Ash didn't get screwed over, losing to someone who was just slightly better rather than some dumbass who should've been disqualified. While it didn't need Ash's Kanto Pokemon, it was much better than the train wreck of the Vertress Conference
7. The voice acting: Just plain and simple, I prefer 4kid's voice acting rather than the current one.