If you're asking opinions on which trilogy is better, I would vote for Dark Matters, hands down.
String Theory definitely had its redeeming value and I enjoy the books. The writing is really good and they contributed good stories and development. But as a whole, they just didn't work for me. I don't know, something about the story just didn't capture me like I like Star Trek stories to do... I never cared for the Q/Kol storylines, or the Doctor being trapped in with the Nacene. It was all a bit too "out there" for my preferences. The resolution still feels a bit vague and empty to me. But maybe that's just me. Ambitious? Most definitely. And I can certainly appreciate that, but something about it just fell flat for me.
Dark Matters may be a predictable, "by the book" story, but I found it compelling. I enjoyed the whole concept of the shadow universe and following the story of Chakotay and Tom in the other Universe while Khala was in our universe. I enjoyed seeing the progression as Voyager was given the mission to recover all the dark matter and how they learned how to accomplish that. I enjoyed all of the new characters and how they were developed and interacted with the Voyager characters. Having good character development and plots where I feel invested is very important to me in a book. The Dark Matters books delivered in those areas more than the String Theory books did for me. If I could choose to see one or the other turned into a Voyager episode/movie, I would definitely choose Dark Matters. Was it a standard, predictable, safe story? Perhaps. But I still found it to be incredibly satisfying and enjoyable to read.