Hm. My first run on MPrime I only got 4. Perhaps aberrant map generation; I was scanning all rooms with the scanner to make sure I wasn't missing any. I used Numa - the Saturn Rescue mission for the rest as I noticed the rescue room always spawns two. Was getting 6-7 per run but it was still a bit of a pain. I had to run 6 missions the long way to get them. I probably spent 1 hour on that alone (compared to 1-missioning all the others with extras to spare and having had plenty of the Earth drops in reserve).
I see. After the rework I've actually really been liking Nekros myself. Already pre-rework I quite enjoyed the Soul Survivor/Shield of Shadows build but now without the need to constantly spam Desecrate and recast the long animation Shadows, it's far less of a pain to play (not to mention, the Desecrate costs are a fraction of what they used to be). And Shadows summons the Shadows around me so it's playable in more mobile gameplay, and the Equilibrium/Despoil keeps me stocked on Energy even through Soul Survivor. I even tossed two Arcane Pulses on him pre-rework to deal with the absurd Despoil costs but now those don't seem necessary or even that useful.
Here's what I'm running right now:
Augmented Nekros
Good for farm, carries an army, revives teammates instantaneously at a distance and is nigh' invulnerable. Even Terror can hit a whole horde of enemies with the PS though I've rarely found the need to be casting it. Incidentally the Terror augment is the only one that doesn't really have any redeeming qualities.
I was also toying with the idea of using Energy Conversion over Intensify since now it won't get eaten by Desecrate all the time, but I'm not sure how recasting Shadows to max out the shadows' health interacts with it. If I need an energy orb every time I do that, it's probably not that amazing. With Nekros Prime, I'll finally be able to rank that Blind Rage up to 10 and be able to cast Shadows even while under a Parasitic Eximus's energy drain.