@Beau_Van_D
warning, this is one of those times where the issues caught my attention more than the positives. This is more a reflection on the fact that I tend to zero in on things I perceive as problems. Also I got tired from typing so much about them.
Let's see...
This a story with cliches, but cliches aren't necessarily bad. Often, though, it means you have to work even harder to have an impact on the reader.
I think the word that comes to mind that sum up the issues I had with this story is 'generic'. There's a lack of specific descriptions, which is part of the problem. I'm not in favor of infodumping, but I feel like I could know more about this village and this family before it's all destroyed, especially considering they're non-humans in a fantasy world. Details that make it feel like a real physical location with a community would help, along with bits that would tell us how their life is different from a human's.
One of the major things that popped out at me was the lack of names for the village, academy, council and war. There is also little physical description of characters and locations.
So, I tend to just mentally fill stuff in with generic images. Generic Unnamed Fantasy Village. Generic Kindly Parents. Generic Bad Soldiers. Generic Loved Ones. Generic Prejudiced Villages
This also sometimes pops up at dramatic moments, like when Indigo looks out of the cave to see the mage confronting the soldiers. What sort of armor does the army have? What are their numbers? Where are they positioned on the beach? Is there a boat they're they're retreating to? What design of banner are they fighting under? How is this mage recognizable as a mage of the council? Is he displaying his powers in a way that's threatening? Are the bodies of soldiers he already killed around? Is the army cornered? In full retreat? Bristling with spears? Shooting arrows that burn to a cinder before they get anywhere near the mage? I'm not saying all these questions need detailed answers, but saying that an army is retreating from a yelling mage of the council tells us the facts without putting us there. So in my mind's eye, I fill the scene with Generic Mage and Generic Army.
When Indigo returns to the village to see everyone is dead. "There lay the bodies of the people he had grown up with, of the people he had once admired as a child."
While there are details of Indigo's emotional reactions here, and throughout the story, the description of the scene itself isn't evocative of those emotions in the reader.
I hope you on't mind me giving a bit of rewriting a go. Warning, I make no assertions of my competence as a writer.
It's not great or anything, but maybe if gives an idea of what I mean?
The townsfolk seem less like real people and more like a plot device. The town was just attacked. People were, presumably, killed, possibly kidnapped. Houses have burned down. I'm not saying some people might be most interested in killing Indigo, but surely others would be preoccupied trying to put out fires, or heal the injured, or find their children. Indigo speaks of loved ones, but the only named person in the village is his sister.
The same might be said of the director. He seems quirky, but inappropriately so. This village wasn't a great distance away; boys walked from the village to the Academy in less than a single day. If humans attacked and destroyed a village within walking distance, surely the entire Academy would be on high alert, getting ready for attack, comforting students that had lost their entire family, etc. After that kind of mass killing, only a truly awful person would ask a boy arriving on their doorstep why he hadn't arrived on time. If they were suspicious, it would be because they view him as a potential spy or attacker. They'd want to know how he escaped, if he was okay, where he'd last seen the humans. Maybe it was intentional to portray the director as the sort of sociopath who would say " the world is no fun without a tad of mystery" in regards to a young man running off to possibly die, and definitely finding his entire village dead. If he is meant to be that callous, then the receptionist and Indigo should probably react differently.
'Nother thing, the worldbuilding. These characters aren't human, but I'm not clear on exactly what they are. So far, the only power we've seen manifested is the ability to see magic auras, which apparently isn't universal. It seems that most of the other abilities are tied to the crafting of potions. If that's the case, what makes these people different from humans? I guess I'm wondering if anything in the story would change if they were just humans.
The rules on magic also seem excessively harsh. Generally only those with strong religious beliefs that involved fear of demons or the like go full witchburner. This is a culture where everyone seems to be magical/alchemical/a user of magic? Using questionable dark magic or going outside one's gender role might involve punishment or social ruin, but burning at the stake seems way over the top. It's possible to portray the society as being that extreme in its views, but there would probably need to be more signs of that kind of extreme behavior.
Oh, while I'm on the subject, assuming this is a small village, Indigo would know the name of the girl who was burned at the stake, and would probably refer to her by name. Goes the same for most villagers, actually.
This is getting pretty long, so I guess I'll just warn against excessive specialness and excessive persecution. Right now, Indigo is under threat from people who will kill him for being born a woman while attending the Academy, for practicing dark arts, AND for being non-human. He is also already a highly accomplished potion maker who can sense auras and knows things that others don't know about, like the village being under a protection spell. His entire family and village also died tragically (even if it was their fault, something I did like). Too much tragedy numbs the reader, and prejudice can sometimes be an easy way to make a character suffer.