Per the above points:
-I think RJ17 puts it best - even if we accept the Overmind and Kerrigan as sympathetic figures (which I do, and IMO, they're better characters for it), the zerg as a whole aren't sympathetic themselves. In HotS, this is reinforced over and over, from all the characters, and arguably the zerg as a whole. The primal zerg are Darwininian - survival of the fittest, "unclouded by delusions of morality" (thank you Ash). The Swarm are the same, only on a much larger scale. No-one sheds a tear for the billion-plus zerg killed on Shakuras for instance, because they're ZERG, even if they're obeying Amon and not Kerrigan. They aren't sympathetic. There's been interesting zerg characters, even sympathetic ones, but the zerg are, and always have been, monsters. Izsha even outrights states (paraphrased) "you're either zerg or the enemy."
-On the subject of the borg, I can't really comment on TNG or Voyager that much (unless we include sfdebris), but I actually like the borg queen for instance. It doesn't detract from the borg in my eyes, but actually adds to Picard and the Federation. The idea that the borg's foes have actually brought them down to converse on the level of their enemies, as they've proven themselves to warrant that (Wolf 359, Earth again, etc.). And similar to the primal zerg, we have borg outside the Collective (or something, there was a Voyager episode I believe). That, IMO, adds to the borg race, even if the Collective itself remains monolithic (like the Swarm), and a stronger adversary for it.
-Back to Prometheus, I agree that sometimes leaving things blank is for the best. Space Odyssey is one such example. The Flood from Halo is another (for me, they were much more interesting before being revealed as the remnants of the Precursors, even if I saw that coming way back in the Beastiarium). However, Prometheus doesn't give us the origins of the xenomorph (the film establishes they were around before the deacon), and the EU had fleshed them out long before Prometheus did.
-As for Metroid...Other M aside (which I haven't played, only watched a walkthrough, and I'm not going to comment due to how hot the topic remains), speech and backstory didn't ruin Samus IMO. She's been monologuing since Super Metroid, engaging in dialogue since Fusion, and had her backstory filled in by the manga, which was further hinted at in games such as Fusion and Zero Mission. Whatever you may think of her characterization in Other M, dialogue and backstory aren't the issues IMO.