It is impossible to choose based on style alone, both are so cool! XD
Which do you find easier to draw? You should consider the medium, a comic, which means you have to draw the characters over and over again from all different angles. I'd go with whatever is fastest to draw. Comics can become tiring and painful to draw if they take too long.
The ponies from the show can be very simple to draw, but you have more practice with your style. Either way it's going to look beautiful!