Interesting replies. I'll try to address the bulk of the points while explaining the particular situation here.
They do essentially have human motivations (although there are no true humans in this world, more on that later). Their power is great, but it is limited and they do tire if they overextend themselves. Because of their essentially human natures, they are more prone to mental fatigue than physical. They can fall in love, they can nurse grudges, they can get angry, and they can simply be wrong as well. They can also die and get injured, though killing them is hard especially if they see it coming.
They're not omniscient, though they do have some abilities of clairvoyance within their element that can let them fake omniscience to those who don't know their limitations: One can see through the rays of the sun, the other can see in areas of darkness, but both can only look at one thing at a time through either magical or normal sight. Beyond that, they have powerful magic within their domains. The active one has powers related to the moon: darkness, cold, dreams, nocturnal beasts, and, interestingly, hope. They don't have any power outside their domains, but within their domains they are mainly limited by their endurance and creativity. In fact, a good deal of their perceived power comes from the fact that not everyone knows of their limitations.
The active one is just really coming into her power. She's been around for many, many years but has been following her inactive sister's orders for that long. Now she's trying to make her own way in the world and fix some of the problems that her sister's laissez-faire approach has caused. Most pressing at this moment is an invasion by a corsair armada.
The corsairs are from a different species with their own magic. They're extremely tall and slim with extra joints on their limbs, and move something like spiders. They also have a unique form of magic using spirits and alchemy that is as much a paradigm shift to deal with as the Canim blood magic in Codex Alera. I haven't entirely pegged down what they can do, but she has only the barest knowledge of what they are capable of as well. It's quite likely she might try something that makes perfect sense but turns out not to work as well as she thought.
My goal is to make this a difficult triumph for her. She manages to succeed by rallying the townsfolk and by defeating some great personal challenge, thus solidifying her position as a good leader and rival to her sister, whether she likes it or not (long term: not).
PS: To answer the elephant in the room: Yes, this is loosely based on My Little Pony, as hinted in the original post. Very, very loosely. They're not ponies, they're humanoids, and it diverges significantly to the point where it's basically its own thing. Hey, we're on the forums of a guy who put a Pokemon vs. Zerg fanfic on the best seller list.