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I recently read this guide posted in the Unity website about Resources. It is clear from the get-go that it is discouraged to use Resources unless you are prototyping something.

My game is like a 2D RPG, and it has over five thousand monster sprites (yes, a lot). As far as I'm concerned, it makes perfect sense to put all the sprites in the Resources folder, and just load the ones that I need (using their name) when a battle starts and then unload it.

The Unity article makes one point that may support my approach:

Generally required throughout a project's lifetime

Well, I'm not so sure about it - in a single game session it's entirely possible that thousands of those sprites will not be used at all as the player simply doesn't encounter those monsters.

The article goes on to talk about why is it discouraged to use Resources:

This operation is unskippable and occurs at application startup time
while the initial non-interactive splash screen is displayed.
Initializing a Resources system containing 10,000 assets has been
observed to consume multiple seconds on low-end mobile devices, even
though most of the Objects contained in Resources folders are rarely
actually needed to load into an application's first scene.

And it is indeed true - my game does in fact take several seconds to load on some low-end devices, especially Android. And it is also true that none of those sprites of mine need to be loaded at startup.

So I am willing to stop using Resources - but I am at a loss now: the article doesn't mention a reasonable alternative to this.

Here are the (unreasonable) approaches that I have thought of:

Create a component with a collection of all the sprites, that way they are all loaded without using Resources.

Yeah but I have five thousand sprites. This sounds extremely tedious.

Same as the previous suggestion, but use Texture Packer or something similar to pack lots of sprites into different sheets - this way I have to do less work.

My sprites are large and packing them won't be a huge help - I'd still end up with a thousand or so sheets.

My point is, I just can't have 5000+ sprites preloaded. I need to load them at runtime via Resources, but Unity clearly discourages it. Is there a solution to this?

If you want to load assets at runtime, then the solution suggested by Unity Technologies is to put those assets into asset bundle files which you can then load at runtime with AssetBundle.LoadFromFile(filepath). When you don't need the sprite anymore, unload that asset bundle with loadedAssetBundle.Unload().

Putting each sprite into its own asset bundle might be one posible solution. But I have never worked with a project with 5000 asset bundles before, so I am not sure if this solution is really that scalable. If you can, try to group your asset bundles into what you are going to need at the same time. For example, if you have a 1:n relationship between areas and monsters, try to put all the monsters for one area into one asset bundle. But now you do of course need some kind of directory system which tells you which monster is in which asset file (with each monster in its own file, you can just name the files after the technical identifiers of your monsters).

I am looking forward to defeating all the 5000+ monsters in your game.