Concerning the Mutes: I liked how they were developed and still remained alien and 'cool'. And while I'm aware the different ST tie-ins don't need to correlate, it satisfies me that the representation of the Mutes is largely consistent with what we learn in the 25th century about the... Elachi
I had to look that up on the Star Trek Online
Wiki, but I don't think their version is consistent with mine at all. They seem to have conflated the "Silent Enemy" aliens with the extradimensional solanogen-based life forms from TNG: "Schisms," which don't look at all similar -- and which emitted clicking sounds, while the SE aliens were utterly silent. Frankly I think that's a very strange decision on the game designers' part.
Also, as fits the needs of a combat game, their "Elachi" appear to be arbitrarily malevolent and rapacious, while I went a very different route.