"Let me just over-analyse this..." ;)
The game has a good bgm, great pixel-art, the instructions were easy to understand and the controls were smooth. Right-click cheating was disabled and I didn't run into any bugs or stages that looked like they were rushed, even when I looked for them. You took your time and clearly did some testing before you published - the result reflects this well.
You avoided all those horrible, horrible newbie-errors Newgrounds sees day after day which on itself is already quite an achievement.
However there were some minor flaws:
- Before the game starts there's a brief introduction to the whole cutie-mark topic for those who don't know about their meaning in the pony society. But the majority of the players will hit space before they even know it's there. Maybe a little menu with <Start> and <Story> options would help players to notice the additional contend.
- The cutscene-art seemed rather off compared to the rest of the game.
- There were no puzzles. Since it's labeled as a role-playing game I expected a little more obstacles, but I guess it's appropriate for your target audience.
- The boss of the Warrior Ending was really easy to beat but he took forever. Personally I prefer more challenging patterns. You could draw some inspiration from looking at bosses from the Mega Man series. A more complex pattern and shorter live-bars would make the boss-fight more interesting.
Since I played the game several times for review-purposes, I noticed both yours and the boss's firing frequency went up, once a fair share of life is lost. While that evens out the odds, the fight still takes very long if you don't get hit that often. - The game was over too soon. I had fun playing, but felt it ended rather abruptly. I know, "Good game. Make it longer." is a common review these days which perfectly underestimates the effort this calls for. It is hard to just extend a story while keeping it from going bad and while I prefer a short and solid story over a long but far fetched one on any given day, it just felt a little bit too short.
About the different endings:
Warrior Ending: I would imagine most players will get this. While Physical conflicts and "Eat this" don't fit the theme of the original series very much, I liked what you had done with it anyway. Whether the brony-scene will agrees or not, time will tell.
Muffin Ending: Players who have seen the series will figure it out rather fast. The Ending itself was rather wacky but likeable.
Bank Flank Ending: I don't want to spoil too much... It can only be found under certain conditions which might be a good thing. While you certainly worked out some interesting new ideas, there are several things in it that don't fit to the canon. I'm pretty sure bronies won't like it, so I encourage them not to look for this ending. Trust me on this.
Yet Another Ending(?): If there are even more endings I wasn't able to find them. Yet. ;)
All that being said, the above statement is still true: You did well and created a fun game that definitely has replay-value. Thank you for doing so and best of luck for the upcoming Contest.