Is it really truly missing, though? I think it's just at a diminished level, and the series is better off for it. I've watched over 400 episodes within the last two years encompassing the three regions with Misty, as well as almost all of the Hoenn and Sinnoh episodes, and I see the same types of humor across the entire length of the series, though they focus far less on the
slapstick comedy used for humor so much in the early seasons. The move away from more slapstick humor and a focus on the characters they meet is actually an improvement in my book.
As for me, I don't really care whether Misty's in or not. Maybe give her a cameo to update her team every once in a while, but that's all I would be interested in, personally.