I saw this just earlier today on Deviantart. ^_^
Anyway, the idea itself is interesting, to say the least. If someone was told that there was a pokemon fan fic about the stereotypical knight-rescues-princess, this certainly isn't what they would image. They would likely image a story where the knight used pokemon either instead of or alongside his blade. If they were also told that all the characters were pokemon, they still wouldn't think of this- they would be likely to think the princess was some dainty species, with the knight being one of the many sword-bearing pokemon. Heck, even if they were told that it was a reversal of the idea, with the knight as the kidnapper and the princess and prince as dragons, they would likely think the Princess was an Altaria or some such.
But, no. You get an over dosage of creativity points for making the princess a Hydregion, of all pokemon. A three-headed, part-dark pokemon. Now that's creativity. Okay, okay, I'll start on the nitpicking now. -_-
Though I respect you for keeping so closely to the knight-rescues-princess formula, it has the typical downside of being clique- which seems a little sad, as I was certain the princess was going to buy her prince the time he needed after he was knocked down with Flamethrower or Earth Power or some-such. Next, the sizes seemed a little... off. What do I mean by this? Well... You had a Rapidash carry both a Haxorus and a Hydregion, both of which are larger than it. Okay, okay, I'm getting to the end. The last thing I noticed was the description. It seemed a little... distanced. Detail is always a good thing, but you had the reader almost expecting it when you had the narrator introduce themselves as the prince. That part, let me say it, was a stroke of genius- you pulled the reader from a detached, third person point of view to an intimate first person point of view absolutely beautifully. The problem, however, was your follow-up. After you pulled the reader into your grasp, you kinda... let them drift away. The detail after that point was not quite at the same level as the hook. What do I mean by detail? Well...
While this is a respectable paragraph, I personally think it would of worked even better with more detail. To provide a (bad) example...
I came toward him, quietly, planning my attack. Then... WHACK! I hit the Dark Knight hard on his metal plated helmet, which lead to a ringing vibration in his head. We watched as he fell hard to the ground and never got back up.
...Sorry if my example is really, really bad. It's 2AM and I'm really tired. ;_;
Silently, I crept up behind the Dark Knight, stealthily closing the distance between us. As I approached, I glimpsed the fear in my princess's eyes once more- The very same eyes that depended on my protection. I sharpened my resolve, bringing my blade high above my head- Suddenly, I struck, the bright sun illuminating my sword's length mere seconds before I brought it down onto the villain's metallic helm with a dull thud. A clear, loud note rang out as metal met metal, a sound I knew would be reverberated within the kidnapper's skull hundred-fold. The Dark Knight fell to the ground before our eyes, never to rise again, his evil forever vanquished.
I'll see if I can come up with anything better to say in the morning.
"Open your mouth too wide, and your ears close."