Pretty nice -- the levels feel like they should have been made by Parallax, but weren't... well... if they were made by Parallax they probably would have used the keys in a more standard way...
It seems like you also paid a lot of attention to making sure the default midi music fit into each level -- which IMO should be done for any mission that doesn't have a custom soundtrack.
I attempted a hotshot playthrough:
I had some trouble solving level 1, but it was very well done, and I really liked that matcen corridor (the one in the mission screenshot).
Level 2 was awesome. Definitely the best of the three. It feels D1 First Strike, even though it doesn't really feel like any of the levels from that mission. I didn't find the secret exit, because I only looked at the maps in the editor after I had tried a playthrough -- I wanted it to be fresh.
It looks like on the first two levels, the blue door leads to either a secret or the hostages. I wasn't able to get either of the blue keys, but I think that's a cool idea.
Level 3 I was game-over'd in the boss area before actually facing the boss, but there was some nice design there too. I just didn't get to see all of it. Overall I think the intro area wasn't done as well as in the other two levels, but the rest of the level had the best design.
I have one small criticism/suggestion for you though -- this is something that bugs me about a lot of custom levels and levelsets:
I don't like having doors on flat walls. There are two major reasons why you might want to consider putting doors in recessed alcoves on the wall (the way they were done in the Parallax missions).
1. You can put the lights around them to tell the player how they're supposed to open it. Any door that needs a key should always have the lights around it unless keeping track of which door is which is a planend part of the level's challenge, or you let the player know in some other intuitive way (warning stripes around key-requiring doors are confusing, especialy when it's a yellow door -- because usually the yellow stripes can be used [and were used in First Strike] around doors regardless of what the door is. Blue and red stripes also are sometimes put around regular doors in the Parallax levels IIRC, but that's less common).
2. Putting the door in a recessed alcove gives it an illusion of having 3 dimensions instead of 2.
When you play through the Parallax missions it's pretty obvious that the level designers had some rules they were expected to follow while designing the levels -- they did bend them sometimes, but that was rare. If you want to make an authentic looking level, one of the best strategies is to figure out what the level deisgners' rules were, and stick to them. If you're going for an experimental or surreal feel, then figure out those rules and break them (one of them or all of them or any number in between) at every opportunity
. And sometimes it works to figure out the rules, and then while you're planning the level, decide on a few rules you're going to break -- maybe to define a new concept or add a new game mechanic -- but do it consistently, especially when it involves level flow. Parallax did this in the Vertigo mission -- a good example would be the second secret level, with the huge doors that open when you approach them, and it was done consistently -- when you saw those doors you would know they would open automatically when you approached them, because they always did. A lot of the best user-made missions also seem to have used this strategy...