I have decided to go with Abra, as it is one of my all time favorites and fits with the team Mystic thematically. Well, that was not such a great idea. The humanoid shape of Abra was a pain to represent with a single color. I ended adding a slightly darker blue to break the monotony and the flatness of the figure. It is still a little too busy for my liking, but until I have more time, it will have to do.
Apparently there is some confusion about the exact shape of the team Mystic emblem. At first glance it looks like a hexagon, because our brain fills in the parts obscured by Articuno. Upon closer inspection, it is actually a shield shape, as explained in this image. So I made my emblem shape by tracing that graphic. It was also handy for getting the exact shade of blue.
Placing the "meditating" Abra outside the emblem adds a little more of the mystical flavor to the badge. As was the PokemonGo logo/marker above him; it can be represented as a map marker, or a "third eye" of sorts. It is far from perfect, but the lack of time and the fact that I will probably print it only as small stickers that will hide most of the imperfections, makes it good enough for now