Here are a couple suggestions:
1. When you place a tile or entity in the map editor, why not place a small number in the tile/entity's upper-left corner, telling the user what layer that tile is currently on. A feature like this is implemented in clickteam products. This could make editing a bit more stream-lined for quick layer identification. It will also help prevent users from accidentally placing an entity too high or too low.
An example might be:
User places a tree, which consists of the trunk tiles, and then the tree leaves. The main part of the tree will be placed on the same layer as the 'trunk' anyway, but the edges of the trees' leaves will be one layer higher. However, if a user has infinite layers in future versions of solarus, and may need to move a tile to a different layer temporarily, they may forget to return a tile to the layer it needs to be and it may render incorrectly at runtime.
2. Having the ability to copy/paste or duplicate tiles in the tile editor. It would be a lot faster if you had the ability to draw tiles, select one or more tiles, and then paste them to new locations on the tile sheet for a much faster tileset creating process. If a user has a tileset that contains duplicate, but recolored tiles within the same tileset, copying a completed section of the tileset, then pasting that new data into the unfinished section(s) would exponentially speed up the tile making process. Size, animation type, default layer, and path properties can also be transferred to the pasted tiles.
1. I understand the problem but I am not sure about the proposed solution. Putting a small number on all entities is too much visual noise.
Also, remember that you can show/hide each layer very quickly with keys 0/1/2.
2. This is a feature request we already have in the bug tracker. Solarus 1.4 already improves this by allowing to change properties of multiple tiles at once, but I agree that we can do better.