When Factorio was using simple 2D hand-drawn sprites for most things, a 2D-based engine was fine. But now that most graphics are 3D models, it's a major waste of space to use them as pre-rendered 2D sprites - with no mods installed in 0.8.8, the texture atlases are over 370 MB uncompressed. That's insane.
Every computer with 370 MB of video memory (i.e. every computer that is not really old) should easily be able to handle the original 3D models, which would also take up much less space on disk and load faster.
Advantages of using 3D models:
- Lower video memory requirements.
- Faster loading.
- Smaller file size.
- Allows for more dynamic effects - for example, shadows could change as the sun moves across the sky.
- Allows for more consistency - several parameters, like the light direction, must currently be "baked into" each image. If the game controls the light direction, there can't be accidental mismatches.
- Simplicity.
- Allows for more complicated graphics - what if someone wants to make an impossible triangle sprite, for example? Averted if both are allowed.