Personally, I've never enjoyed doing Deep Space Encounter missions. Waste of time vs. rewards overall. They are repeatable true, but I'd rather go do the Exploration missions myself. Better rewards, better variety of different mission types. I personally feel Cryptic should setup them up similar to Exploration missions where once you do one of them, you have to go do a regular mission in order for the Exploration mission to be available for repeat.
Far more creative and far more compelling would be to mix in some mission content within the star clusters.
For example, do 10 "regular" star cluster missions, then you get a mission where you find an old starship, dead in space. You beam over and find all the crew missing. You find a clue that takes you to another planet in the star system. You beam down to discover that the crew had been abducted by an alien race that now seeks to inflict this fate on your own crew!
Successfully complete this mission then have another 10 or so where you go on a scavenger hunt for special rocks on the ground. This way, you never really know what you're going to find when you warp into a star cluster system.