The spawn times definately need to be lengthened. This has been discussed in other threads, so I'm not going into it here. I'm pretty sure we can all agree on this one, regardless.
There should be a 2 or 3-Tholian limit on how many can be attacking at once (outside the boss battles).
Tholians outside the area shouldn't be triggered to attack. I've noticed that sometimes one will essentially lure me to an area with several more and I'll be completely overwhelmed in the span of a few seconds. Other times, I'll be fighting one group and another one will wander into my area, triggering the rest to follow. This makes it almost impossible to finish the meduim missions, primarily outside, but this is inside in some areas, too. Putting boundries in their wandering zones would solve this problem. Just go to any random star cluster planet and you'll see what I mean. The enemies are in groups, seperate and don't trigger eachother. I don't think this amount of distance is necessary, but it's the same basic idea.
We should be either invincible or ignored when we're mining. That, or shorten the mining time from 60 seconds to 30. It wouldn't be a huge difference with the spawns, but at least we'd get more then 5 or 10 pieces each time.
There should be some loot (like the Deferi Invasion) other than the mission-spesific stuff with the OCCASIONAL bit of random loot. I've noticed when I finish a mission, the vast majority stop dropping loot. Why not put white and green versions of the blue and purple stuff we get in the boxes into the drops to make it more interesting? Maybe some sort of limited crafting like Defera? That at least would make that huge kill number seem less tedious (exchange loot=EC).
I also think the 375 mineral/kill requirement is a bit steep for the 10/15 marks we get. Given the difficulty mining at least, I think the limit should either lowered, or the mining made easier (see above).
For the internal missions, I've noticed there are A LOT of higher level Tholians in one place. Ones I start attacking one, I get attacked by, at a minimum, three more. In these areas, I think the tholians themselves need to be spaced out and have their spawns slowed. For the external missions, I've noticed that it's hard to activate things (or pick up items, for that matter) when there are so many Tholians surrounding me. Spreading them out, and their spawn places, would help with this.
A greater diversity in available missions would be nice. Defera has 3 areas and the probe. All we have at Nukura is inside or outside. Some other ares, like on an island or underground or in some other remote area would help with this limitation. Defera has The City, Temple, and Power Plant (essentially). How about inside, in orbit (a space station ground situation, not a space mission), underwater/underground in a Federation Research Lab (under attack, of course), the Tholian incursion city or base, maybe a Tholian power center or rift control center type deal? There are a lot of possibilities.
When you get down to it, both Defera and Nukura are about grinding. The biggest difference (besides the marks and boxes) is that Defera is full of zombies and Nukura is full of hyperactive insects. They're basically the same. Identical concept, anyway. I think each planet would have some special mission to distinguish it more than easy-medium-hard, boss-rare item-start over. The grind on Defera is a little worthwhile with the crafting, but it can only go so far.
My biggest complaints about Nukara is the fast respawn time, Tholians having an odd aggro (coming from across the zone to attack you), and the horribleness of trying to Mine the Crystals (which is a pain since you are under constant attack).
And like said above, it gets boring fast. The only thing to do there is farm Marks (during the event) and collect the sets, which isn't very good since STF 2-Piece is more effective.
Also be nice if there was something extra for doing the Hard Missions, since you have a better chance of drops by doing the exterior medium missions.