I used to be a slush-pile reader for a Science Fiction and Fantasy magazine called Absolute Magnitude. Just so you know, you've already passed the mark for 95% of all our submissions. That is, 1) you can write in English, 2) you can write whole sentences (with nouns, verbs, adjectives, and adverbs in all the correct places!-- and yes I did see a few submissions where verbs were dealt with only rarely.), 3) you understand punctuation and paragraphing, and 4) your dialogue acting sounds like people talking and not robots.

All you have left to do is write an interesting, plot-driven story. (And THAT'S the hard part!)

As for POV, I think you only really need three: the colt, Luna, and the Colonel Sprite. The General serves no real purpose except to form a connection between the Equestrians and the Sprites. All of his interactions could be handled as what the Colonel hears when the General reports to the council. For any "private stuff" that the Colonel won't be present to hear, well, that's what spies are for, and the colonel already has one reporting to him. Just add a few more. Things that the General does that you don't want the colonel to know are done when there are no spies around -- and kept secret until the colonel trips over them. And there can be counter-spies and double-agents as well, if you wish.

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BTW, tracking the colt shouldn't be that difficult. As many bandages as he has, most people would have noticed him moving around the city, especially the ones working as police. They quickly would have determined his singular route and be hot on his trail.

In Chapter 5, everything that Celestria thinks could easily be inferred or said out loud to Luna. Even the scene of her on the balcony could be a conversation ("how was your morning?" "Fine, It was very peaceful, a rare event now days,..." and so forth) There really is no need to include her POV. The more POVs you include in a story, the more difficult it is for a reader to stay focused on YOUR MAIN CHARACTER.

Walking out of the throne room, Storm Front’s mind immediately turned to what he would do with his pass. As he turned the corner and headed for the barracks, he found himself hoping that his sister Silver Streak had gotten back from her latest long distance run for the family delivery business. Figuring that she probably had, he found his pace quickening until he was almost running down the castle’s halls. It would take him ten minutes to stow his armor and shower, half that if he rushed it. Sensing an invisible clock ticking away in his mind, the stallion broke into a gallop. Thanks to a pair of extended training exercises and this run, he hadn’t seen his family in over a month and it would be nice to go out to a restaurant with them to catch up.

The above does nothing to move the plot. It can be removed and never missed from the story, as it has zero impact on the story. It should never have been included. All it does is slow the story down with uninteresting fluff.

If you truly must include it, can't bear to leave out such a wondrous bit of pointless exposition, change the POV to Luna and have her mushing about how he was one of her first appointments to the messenger and make it her thinking that was probably what he would be doing.