Also submitted by edgehypermatter:

You have been warned before, it bears repeating. Do NOT mess with the one known as The Doctor. Yes, he's goofy, and the closest thing he has to a weapon is a sonic screwdriver. DO NOT BE FOOLED. His true weapon lies inside his head. He is monstrously clever and is capable of outstanding cruelty to those who anger him or harm those he associates with. If you get on his bad side, being banished to the moon for a thousand years will seem like a week long vacation on the beach. He won't kill you, he'll find something much worse. Fortunately, he usually gives you an opportunity before he utterly crushes you. And that time is usually right when you think you've won. I suggest you take it. No matter how bad off he seems, if he's offering you an opportunity to walk away, it means his trap is ready to be sprung and if you scorn his offer, there will be no escape. His previous victims have been trapped in black holes, mirrors, erased from time itself, and trapped in the space between dimensions, just to name a few. If you value your continued existence, you will not trifle with him.

Submitted by edgehypermatter:

These are just thoughts that are in no particular order, and may or may not be helpful to you.

You probably already know this, but in order to defeat the elements of harmony, you're going to have to drive them apart. After which you could probably deal with them at your leisure. Here's a little help. In order to defeat the one known as Pinkie Pie, you must first get ponies to stop coming to her parties. If she's under the impression that nopony likes her parties, she'll fall into a deep depression and madness. I've heard to this referred to as Cutie Mark Failure Insanity Syndrome. The biggest obstacle to this goal is the other elements of harmony. I would suggest causing "accidents" to happen at her parties. Poison in the punch bowl, poison in the snacks, things falling on ponies for no explicable reason. Be warned! They will investigate the mysterious happenings, and if they so much as catch a whiff of your presence, well, I don't need to tell you what would happen.

Understand that the primary difference between being loved and being feared, (And I am aware, the two aren't mutually exclusive), or at least how it relates to you, is how your subjects react to rebellions. A loving populace will quell a rebellion, whereas a fearful populace will join it.

The best way to usurp your dear sister is to turn her subjects against her. If all her subjects call out for her to leave, she most likely will without a fight. This will take time. You will need to be patient, because if you do this too quickly, somepony will catch on and ruin everything.

Be careful out there.

We thank you for you advice (this is how productive We wished all our subjects were). Some very good ideas there, especially regarding the Pink one. We still aren't sure on the whole love/fear dichotomy, but We will take your thoughts into consideration.