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!
I like quadrupedal ponies, but that doesn't necessarily mean "official style". Cartoon style is simplistic because of the technology used - I still like it, but there are artists whose style I like more than the cartoon one. I'd have absolutely no problem with your anthro style, though. (I mean, why would I? Your anthros are a thing of beauty). One of the things I like Equestria for, is the fact that it's dominated by quadrupeds - I like how people come out with interesting designs of everyday items etc, that accommodate to this fact.
I selected your anthro style because since this is a fan ending of your own story, it be kinda suited to it. Yeah it's same logic for either option since it will be drawn in your style but since it's your story why not draw in a way you're comfortable with?
Plus, I also selected your anthro style 'cus it's cute.
I'd like to see your anthropomorphic style, because your unique style is really the reason I'm following you. I can find tons of MLP art in the original style, but I prefer to see it in different styles.