Harvest Chaser isn't especially endearing as he seems not to care that much that his parents died and simply declaring that he is unpopular doesn't really make it so especially when you have him making out with somepony in the opening paragraphs of your story. Awkwardness and timid behavior aren't especially good reasons to loath a person. Bully, sure, but not despise. Besides that Harvest sounds like a valuable member of the stable being a clearly gifted chemist which just makes it that much stranger when the Overmare makes a snap judgement just like that without hearing him out. What you have here can work but you need to expand on it. It would also help to cut down on the constant monolingual of his 'fluff thoughts' and excess information.

Example: This paragraph is way to long for what it communicates. I'd advise you picture this moment as a scene in a movie and describe it.

"I took a place in the corner and started eating the dish. You know, down here - everything is made of apples. Really. Apples, apples and apples. Apple pies, apple casseroles, apple ice-cream, apple crisps, apple fritters... Continue the list. Only sandwiches don't contain apples down here. I guess apples are such a common ingredient because they were meant to be the real food source, or something. Otherwise there wouldn't be a place, such as the "Apple Garden" on the Stable-Tec blueprints I got the chance to witness a few times. The casserole itself wasn't the most tasty thing, actually. It felt like I was eating water mashed up with apples and turned into a solid substance. Or maybe I indeed was eating water mashed up with apples. Who knows? I've never shown any particular interest in cooking in the Stable and what the foods are really made of.

Shortened:

Levitating the plate of casserole in a sheath of golden light, I paced to a corner booth and took a seat. The steaming watery homogeneous mass tasted about as appetizing as it looked and without the lunchmare's earlier insistence I would've easily confused it for apple pie or apple turnover or apple...
"Ugh..." With disdain, I took another bite as my taste buds rebelled and doubled my efforts to imagine it being anything else.