I am not going to choose for US, but just President in general. It is a very difficult choice.
I know I will not choose Rainbow Dash. Sorry, but I don't think she will be fit for the job.
I like Pinkie's philosophy of making everyone happy, but again don't think she will be able to execute it. I would love to see Rarity everyday for 4 years in the news! But I think she would be better as vice-president.
I am not against alicorn Twilight, but I don't think Twilight's stress or micromanagement will help her. Our world is too complex and if she can control EVERY SINGLE THING, she will FREAK OUT. While Fluttershy's policies would be to my liking, the Senate would probably reject every bill of hers and she will not fight back...That means I vote for the best of the best... Applejack.
Congratulations President Applejack! However, if I could choose any MLP character, I think I would vote for Starlight.