All foreground and background layers should be used to compliment the level with eyecandy. And I don't mean like foreground lightning or rain. I mean things like if the tileset has trees, you can create a forest with the background layer and layer 4. Foreground layers can be used to make stuff actually happen in the dirt. I mean, dirt in tilesets is just firing away wasted eye candy space. You can add some extremely complicated and detailed platforms, ledges, et cetera in any area where you can see a lot of dirt tiles. This is incredibly important for tilesets which lack untextured dirt like Islands in the Sapphire Sea or Agama's Swamps.

Also, use every tile in the tileset you can. If you have multiple ground types, then there should be multiple grounds in you level. If the tileset is available with it, why not use it?

Finally, biggest thing that annoys me. If you have a textured background:
1) Don't fade to black
2) Don't use layer 5
3) Make it auto-scroll
4) Try and cover up the weird inverted clouds at the bottom

The point is, a creator needs to be able to weild everything JCS offers to his advantage. As far as level design itself goes, there is no real way to define what makes a good level good. But I try to picture a few things when I work on a level. I picture a bell curve of flow, with one end being rough flow, and the other being smooth. Rough flow is where you bump into walls all the time, and if you jump you hit things, and a sux pile. Smooth is where the level does everything for you and practically eliminates player control. Neither are good, for obvious reasons. If it's rough, people will get frustrated because they can't move. If it's smooth, people will get annoyed when they try to go one way, but the level makes them go the other way. Anyway, the ideal is a situation where the level dosen't force the player to go anywhere, and they can choose to backtrack and won't have to fight with springs. There still should be some rough to navigate places, especially ones which lead to important items like carrots.

Also, final thing that comes to mind is player choice. Levels are roughly divided into "Passages" and "Rooms", although sometimes it's utterly unnoticeable. Every room should present at the very least, a choice of 2 directions to go. The passages are how you get to the next room to make your next choice. This sounds extremely limiting and it might feel as though it can only produce cramped levels with hallways and it'll suck. But basically all jj2 levels, or at least good ones, operate with this sense of passages and rooms.