a) use several planes layered over each other
b) combine the specific regions of the atlas texture to a unique texture
You stated that you do not want to use a), but depending on your needs it may be the better solution. Basically with a) you got to render more, but planes with sprites on it are dead cheap. With b) you only need to render one texture BUT you need to create a new texture for every combination of character and equipment, which is both heavy on CPU and memory.
Tell me if i’m right : i may change the shader in a way it uses uv1 for a second texture, then combine both textures, right ?
But this way i would be limited to 2 textures ? (or 3 if i also use uv2)
Yes something like this. You could use only 2 UVs (because of unity limitation); for more “textures” you could use tangents for holding additional UVs.