Baffled by indecision...

The topic kind of speaks for itself. I'm having trouble deciding on what the central conflict for a journey fic I'm working on called Feral Legacies should be. The story takes place in a fake region of mine called Ronac and involves a shy young boy who's been selected as one of three youths from his hometown, an island city called Maritide, out of numerous others who participated in an annual online Pokemon course to become trainers out of the region's top Pokemon Science academy (as in, a school for people who want to take up careers as Pokemon scientists, but it also serves as the starting place for a select few seeking to become trainers, like I just mentioned).

Anyways, what I'm debating on is whether I should center my fic around how this kid suffered from a horrible incident a few years beforehand involving an attack from a deadly forest predator (a fakemon of mine) that almost ended his life, but ultimately led to him being afraid of Pokemon that are similar to real-life mammals, the creatures that dominate most of my fake region, and how he thinks that becoming a trainer will shirk him of his fear; or if I should have that take kind of a backseat and have the story centered around two of my fake legendaries that are supposed to symbolize the opposition between mankind's advancements in technology and how nature will always try to suppress it. I'd like to use both ideas somehow, but like I said, I can't decide on what to have as my central idea for it.

You can do both. There's no rule stating that you can't have both an external and an internal conflict. The most obvious course of action would be to use the incident to develop your character while he gets wrapped up in this whole legendary thing, but hey, it's your fanfic.

You can perfectly use both ideas.

I'd say it'd be alright if you first centered the story around the protagonist. The second idea can come as a later topic for the plot after you introduce the academy.

Also, remember you will have to apply the most detailed descriptions as you can, considering there will be a lot of fake pokémon.

I thought I could do both, but I wasn't completely sure really how to go about it. What I was kind of leaning towards doing was what you both suggested, where I introduce the incident that happened to the main character first and as the story progresses get into how there are all kinds of stories about weird experiments that go on at the academy in the fic, the most well known being the creation of a unique Pokemon (one of the legendaries) and how when it developed to a certain point the other one was summoned to destroy it. Also, yeah, I'm gonna make sure to describe these things as well as I can. Thanks for the advice!