Why I think AppleSparkle is the most likely ship in the tv show.
1. They are usually the most level headed of the mane 5 and if one of them does start to loss it the other could stop them before they go to far.
2. I think Applejack would be a good step-mother for Spike and could fill the role of a farther figure while Twilight would probably provide a bit more discipline for Applebloom who never seems to be punished no matter what she does.
3. Both of them are workaholics so they would probably be more understanding to the other's obsession.