Let me preface this by saying that my top five favorite ponies are Rainbow Dash, Rarity, Luna, Celestia and Derpy Hooves. All in that order, except perhaps Derpy, because she's no longer canon, she doesn't really have the same ranking system as the others. I'll start the list off with these four (not Derpy), then make an actual list.
Rainbow Dash is my favorite pony for several reasons. The first being that she's one of the most imperfect ponies on the show, yet her success is almost unrivaled. While she may not have the most visible character development, you still have to think: you can't fake awesome. Her character is defined literally by how cool she is. For her to even be remotely feasible, she has to be genuinely great, which is really what she is. She's so great by her own design that she even makes you feel good about yourself when watching the show. For that reason, she's my favorite pony, however I must also remark on how cool her color palette is. Rainbows have long been symbols of difference, and a recent gay symbol. Even though it's just fanon, one can instantly look at Rainbow Dash and see she's clearly not straight. This gives her character depth, a depth that in turn gives the show the depth that brought it to such popularity amongst people not in it's target audience. Not only can you say she's the most important pony to the actual storyline (because of the Rainboom of Destiny), but she's probably the most important pony to the show's success as a whole. Even if you don't accept the whole “gay” deal, the Rainbow is still a symbol used by Ronnie James Dio in a lot of his music, which really brings a lot of the same flavor, so it still goes over well.
Pony number two is Rarity. Most people think I'm joking when I say this, but really, she's pretty great if you think about it. No other pony is quite as real as Rarity is. She legitimately feels like a person you could meet in real life, which is really something, even for non-animated shows. Again, I love her for her imperfections, which are filled perfectly with loads of character development, even to the point where she had the first developed relationship between her and Spike (which isn't just fanon). Sure, we had the Cakes and such, but they were already together by the time they were first revealed. If you watch the first episodes, you can see that Rarity barely has time for Spike at all, but they slowly grow together, and eventually (in the Mare do Well episode) things finally develop into a real relationship, which continue on though the series (as referenced in later episodes). I think she may have gotten the most development of any character on the show, even over Twilight Sparkle, who the entire first season was devoted to. That's why she's such an interesting character to me, only slightly lower on the favorite chain than Rainbow Dash.
Luna is a cool pony, no doubt. She's actually gotten some of the most visible character development, even though she's only been in a few episodes. She was the series's first villain, and as such, you really get a feel for the entire revenge bit. You realize that she's a strong willed, greatly-designed character over all. You really feel like you're watching royalty in the episodes she's in. Her palette slightly changes over time as well, in the second episode, after she gives up the idea of revenge against her sister, she's a small pony, possibly like a Jekyll and Hyde reference, but backwards. She felt the good growing inside her to overpower the bad, and it manifested smaller than normal since it was just then developing. As the series goes on, she's later shown with a fuller build and a much more magnificent palette, which is made to signify her ascension to her former glory. The physical growth of her character easily puts her at this point in the list.
I don't really know why I like Celestia so much. She's not a hugely changing character, but she's so much of a storyline key. She has a huge sort of Dumbledore like feel to her (especially in the Season Two finale), which gives her some definite flavor. You can also see a bit of a backstory with her and Luna, what with Celestia locking her away for an ungodly amount of time in solitude on the moon. You can see that while she's been put on a pedestal as their sort of deity, she's not perfect in the least. Its good to be able to tell that she knows that her choices haven't always been the most considerate, but you can feel her aquired wisdom oozing out.
Now that that explanation is out, I'll explain the rest of the immediate cast and perhaps why the haven't made the list.
Twilight Sparkle: I definitely like her, don't get me wrong, but I seldom prefer main characters. The development is definitely there, though. I know it's not a good reason for not including her in the top five, but it's the only one. She'd definitely be in the top ten. I must compliment her color palette here as well. Purple has almost always been my favorite color range, and I must say that this appeases me greatly. She was the first pony I saw, and I instantly fell in love with her colors. Of course my inner metal-head made me love Dash a little more when I saw her, I still love this one.
Fluttershy: I'm really not a fan of her. She's all based on her cuteness, but unlike Rainbow Dash's awesomeness, it's not her defined character. She's a timid personality, which translates to cuteness to the fans (us). This is all well and good, but really it's all she has. Every episode based on her gives her definite development, but then that gets thrown out with the following episode. Just look at The Incredible Iron Will vs. Hurricane Fluttershy. In Iron Will, she found out how to stand up for herself, and became a stronger person. This is immediately forgotten because they literally deliver the EXACT SAME development in Hurricane Fluttershy. In the early episode with Photo Finish, she was the center of the episode, but it all just turned into development for other characters, especially Rarity. It's like she's the bane of developing. The fact that they actually undo the character development they give her, which is something they don't ever do for any other character, makes her actually about my least favorite character in the series. Besides, the show is already a trip to cuteville anyways, what with the crusaders and such, she really has nothing going for her, in my opinion. Every scene she's in is pretty much the exact same, which really just gets horrendously boring after a while.
Applejack: I like Applejack. She's hard working and such, but she doesn't really develop. It's not really the same kind of fault as Fluttershy, its just that most of the episodes she's in are mainly to develop Applebloom and the Crusaders. It's unfortunate, but I'm sure it'll eventually change in later episodes.
Pinkie Pie: She's kinda like Fluttershy in the lack of change, but thankfully her personality is strong enough to support it. While this keeps her off my list, I must praise her for definitely being one of the most physically moving characters, right behind Rainbow Dash. The little development she gets is also quite nice.
The Crusaders: The three can be put together, all of their development is generally for all of them. I like them quite a bit. Applebloom was actually on my list for a while, but I currently find myself enjoying Scootaloo most of all. Their point is just their crazy antics on their journey to find themselves, so I think they're definitely accomplishing the point they're trying to make. Only problem I find with them is that as child-like characters, I think they should get an unusually high amount of development, which they haven't seen. I'm sure this will change with time though.
Cadence and Shining Armor: I like them both, but they're definitely too new. Two episodes isn't enough for a proper ranking.
Chrysalis and Discord: I love them both. Definitely two great villains in their own respect. I felt a few missed opportunities to tie Discord back in, but it's forgivable. Both had such greatly-designed characters in so few episodes, but the fact that they were only in two each keeps them off the list for me.
Well, I quite enjoyed that, and I hope you did too. I'm sure I'm In for an earful about my strong dislike for Fluttershy, but whatever. You guys should post your own ranking systems. I'd certainly like to read them!