This is something I've been trying to answer myself for a few days now, although I thought I should try to get help from some people, while including the things I've learned, so people can correct me if necessary.
1. Abstract shapes are important. Don't just have a long stretch of land with enemies on it. Have a bit of cover, hell, put it in the air, if you want, and keep height-variation at near maximum, while still having the terrain be traversible and understandable.
2. Good "Target Priority". What I mean by this, is don't make every enemy in the map the same. If it's the start of a level 1, then sure, you can do this, but don't keep it like this for too long. Edit: Just realized this was a bit too vague. I mean, give some enemies (with a changed skin of course, so you can quickly differentiate targets, and threat levels) more health, or, instead of that, different weapons. Or, what's most likely the best option, both.
3. Barrel placement that you, or enemies, can take advantage of. Put barrels around groups of enemies, or where multiple enemies will walk along. Of course, don't always do this, because it might get a bit too easy. Or, put barrels on the player's path, or around. Of course, they can just destroy them, but I still feel like this adds to the map.
4. Make sure there's no "Fake" difficulty. This is probably the hardest thing, at least for me, and something that no matter what game I map in, having real difficulty is always something I strive for. A good example of what I think is fake difficulty is actually within a few official levels. There's been multiple times some guy with a railgun has just kinda shot me out of nowhere. Try to avoid this. I'm not saying not to give enemies railguns, but try to put them in a spot where players will be able to see them at almost all times.
Level 2 does a lot right, in my opinion, and is one of my favourite levels.