1. I'm a bit iffy about the anime Cilan. I feel like he's too different from his game persona. In the games, he's a bit nervous and shy, but in the anime he's outgoing almost to the point of being pretentious. I've met a few people who've agreed with me.
3. I really hate how they portrayed Skyla. The game Skyla is very good-hearted and understanding. She even goes out of her way to help an injured Pokemon atop Celestial Tower. The anime Skyla, on the other hand, is rather stuck-up and immature. She denies Badges to Trainers who can't keep up with her. I was very disappointed when I saw that. I couldn't believe seeing one of the nicest Gym Leaders given a personality more like Lt. Surge. And come to think of it, I wasn't thrilled with how all of the Kanto Gym Leaders (except for Brock and Misty) were portrayed as jerks. Sure Sabrina isn't the friendliest of people in the games, but at least she doesn't stalk you after you can't beat her. I'm only glad they didn't do that to my beloved Morty.
3. Ritchie. He was annoying.