Let's break this down:
Fluttershy: Terrified of saying the wrong thing, and we have seen she hates being in a position of power. (Green Isn't Your Color). Would probably be scared of offending people, and would completely lose her head in a war or political struggle. However, we have seen she is working on being assertive and is capable of standing up for herself. (Putting Your Hoof Down). 3/10
Rainbow Dash: Strong and loyal, would probably make an excellent ruler, but a poor strategist. Still has an amazing amount of maturing to do, but will most likely form long-lasting alliances. However, keeping peace may be a difficulty with her, and we have seen pride go to her head. (Mysterious Mare-Do-Well). All in all, definitely a short-list name. 6/10
Rarity: Seen excelling at running a business (A Dog and Pony Show, Sweet and Elite, etc.,) and therefore would be good managerial material. Is capable of managing other people well and making other ponies like her, despite giving orders (Green Isn't Your Color). However, is very emotional and prone to breakdowns (Every Episode Known To Mankind). Would probably go insane in a crisis. 8/10
Pinkie Pie: Do not consider. Would make a terrible ruler. Equestria would be in total chaos, anarchy would reign, and the entire world would be bathed in the light of neon pink. 0/10
Applejack: Hardworking, honest, and capable of handling huge amounts of pressure and work. Most definitely keeps her head in a crisis, although would most likely be unable to compete with the finer games of politics. Would make a very good, down-to-earth ruler but has been known to be prideful (Applebuck Season, The Last Roundup). 9/10
So it would probably come down to Rarity or AJ.