File structure is probably easier to customise, you could even implement a custom resolver if you like - but first look into pod structure for your routes, which is a really nice structure.
Initially, ember-cli was a nice tool to use with ember, but gradually it has been transitioning to the only way possible to use ember. At this point we’re slightly past the point where it is a very bad idea to start a new project in ember without it, due to missing out on almost all the great things in the ember ecosystem that depend on it.
People may not like the decisions it makes for you, but that’s pretty much the point of an opinionated framework. My advice at this point is to decide if you can live with the decisions ember-cli makes for you. If you can’t, then frankly you are really better off choosing a different framework at this point - that’s my opinion based on the current state and future plans that I know of.