I loved the Gre'thor missions personally. I thought they fit really well.
**shrug** Each to their own. Personally I hate Religious and fantasy plots in Sci-fi. Especially if its not logically explained (Galatica, I'm looking at you!).
Of course bugs and bad level design which the Devs should have known about are a different matter. For example, Areas that are instant kill and you want us to fight next to. Please erect a safety barrier! As you know full well the players bridge officers are going to go over the edge at some point. Either by enthusiastic rolling or knock backs.
This has been an issue since the launch, and possibly the Beta stages, with the Fire caves mission, so its not like it'll come as a surprise to any one.
Don't get me wrong the missions where nice visually, and had an interesting dynamic, but they'd have worked far far far better in a Fantasy game.
Myself, while I'm no fan of fantasy sci-fi, I've never minded and often enjoyed sci-fi with religious themes, plus I rather liked Galactica.
However, I'm not a fan of the Gre'thor missions simply because it's not "Trek".
Every sci-fi setting has its own set of "rules" for what's allowed in that universe. It's these rules that make Star Trek distinct from Star Wars, Galactica ... etc. Now, Star Trek's "rule" about gods & demons is not that different from Conan's. In Conan you never get actual spirits, you either get total fakes or else exceptionally powerful creatures that use their extensive knowledge and abilities to impress their will onto the gullible or defenseless.
The Gre'thor missions just don't feel like they really fit well under the "rules" of the Star Trek universe.
One would think that all of the infiltrators in/on the High Council were all exposed. That being said, why not have an intro/tutorial mission where the player exposes a few Undine. It would give the player an opportunity to fight Klingon facton sprites(they were dupes, weaking the Empire, culling them makes us stronger), and activate the Undine Kill accolade(Tripod Terrorist), wheting the player's appetite for more.