So, you'd like to have some sort of random mission to grind specific mobs and XP.
May i point you to the fleet missions? Random species, to shoot at and grind both xp and accolades.
They are also very repetitive, so if you enjoyed the repetition of cluster missions, you'll love those too.
in other words, what you are looking for is already in the game. Don't say you didn't mean that, because that is exactly what your post asked for.
as stated many times by various devs in interviews, the devs want new players to advance in levels through story missions.
never talked about STFs, since the fleet missions are low level too and provide exactly what you asked for in your first post. And yes, you can actually create a complete private instance for only yourself.
If queuing and playing with other people in an MMORPG is something you do not want to do, then maybe a MMORPG isn't the game for you anyway. It is called Star Trek Online afterall. What i mean by this, is that it is not the fault of the devs that they tend to offer more grp content than single player content.
I miss the missions. It was a break from the constant STF grind. You would start a mission and right off you could be jumped by Reman warbirds! You could have to scan 5 particles or solve why ships were being attacked and by whom. You might have to beam down and save a colony or discover a new plant. It was fun. It was a change of pace. It will be missed.
The thing is, you never knew what the mission would be. Yes, there were only so many missions programmed. This was just left from the lack of development time as cryptic was on a tight release schedule. It should have been improved but instead we ended up with a flashy new Earth Space Dock. I find it both sad and disappointing that PWE/Crytpic spent resources that could improve the game on something that is just flash, and half finished flash at that.
Some of my most favorite missions have been removed from the game.
Starbase 24 Rescue (ground)
Foxes and Hounds (DS9 STF)
DS9 Under Seige (DS9 STF)