Take the Targ/Sehlat/Mastiff enemies. Apply a custom costume of, say, Federation personnel, alien race, infected skin... Instant zombies. Why? Because their standard attack becomes a lunge/bite. Set their default out of combat animation to the Assimilated Undine for that lurching quality.
Or if you want a fight kinda like the Gary Miotchell fight from TOS, take a Devidian. Apply a Starfleet officer alien costume that looks human but with reflective eyes. Set the default animation to the "possessed" floating option. Suddenly you have flying, silvery eyed people who fire energy from their hands.
Setting an objective to kill an enemy doesn't mean you have to pull the trigger. Try a mission where you have a large number of hostile enemies behind a wall like the Broken Forcefield. Set a mission objective up so that you're tricking an enemy into beaming into an unsafe place and have them spawn in the middle of a group of NPCs who will kill them FOR the player.
RECREATING FAMILIAR LOCATIONS:
This is for the obsessive among you.
Say you want a mission set on DS9 with the standard NPCs present. You'll need to recreate those NPCs as costumes for use in your mission and manually rotate them to face the correct direction but you can get the overall placement of each character right with the following steps:
1) Take a demorecord of the Deep Space Nine social hub environment.
2) Open it in notepad. The XYZ coordinates of all NPCs will be stored.
3) Use those XYZ coordinates for your copies. You'll need to manually place each mob, manually rotate them, and design a costume for them but you can be sure they're standing in the right place thanks to the demorecord.
USE SETS IN UNEXPECTED WAYS:
Re-dressing a set is a worthwhile skill to pickup.
Want a mission where players beam into the Transporter room?
Place walls and floors in the Transporter area of the Starbase 39 map to make it resemble a ship transporter room. The mini-map will be weird but you get the overall desired effect.
One of my favorites is to take the Generic Federation interior and place turbolifts into archways to block off an empty room and make the endpoint for a map hopping into a turbolift.
It takes time but you could theoretically simulate an entire ship interior using nothing but redresses of the generic Federation maps.
Also, while probably best used sparingly, I think using opposite faction social hubs as mission maps is a lot of fun.
Let the Klingons visit DS9 and help out with a Fek'Ihri infestation. Send the Federation to Qo'noS to uncover a Romulan spy. These maps are generally among the best designed in-game and seeing them from the other faction's perspective can be exciting.