Damn people here (and I guess everywhere) seriously overrating this mess.
I had two thoughts / feelings that recurred throughout the series: "What the hell is going on?" and "I couldn't care less."
There are many elements to the "what the hell is going on?" issues. This mangaka seems to give many characters the same face and only mild differences in haircut. You even see some of the same faces in his other manga. Add onto that similar / same uniforms for many characters, and it was difficult at times to tell who was speaking / acting. The visuals were further complicated by a sort of washed out look, like a photo that has been over-exposed and lost some of its details. This made quite a few panels, especially in the beginning (but even so occasionally on through the end) hard to visually parse.
To further add to this problem, the mangaka often made little or no attempt to clearly set up scenes / situations for the audience. This was especially problematic in the final couple battles where there was little to no establishing discussion among the characters of battle plans or who was part of which unit or visuals of the entire battlefield to give the reader a clear idea of what was going on. A thing happened and then another thing happened, on and on. There was no dramatic tension when I had no sense of the context for some new twist occurring.
Speaking of things just happening, repeatedly throughout the manga, but again especially leading up to and during the final battle, new technology was introduced, things were built, characters said suggestive things, did things, had random personality changes, all out of the blue with little justification beyond "the plot said so".
Finally (though I am sure I could explain more how much of a mess this felt like to me if I took more time) the tonal shifts throughout, from teased (but never explored) political intrigue to space action to romantic drama to comedy, felt all over the place. The pacing was random.
As for "I couldn't care less", well, it's hard to care about characters who, for the most part, are one dimensional at best. Each character could be boiled down to one, perhaps two, traits. They never really develop, though some of them do have abrupt, lurching personality changes or revelations. There were a few characters that I did find really interesting (Lala the space bear, Kobayashi the commander, Ochiai), but they were never really explored significantly.
In fact, little was explored in this manga. It had a lot of potential in terms of setting up a really interesting and provocative situation where you had the potential for tensions between humans and aliens they could not communicate with and between different political and social factions of humans. There are a handful of moments where some clash of ideas or philosophy is teased, but nothing ever comes of it. Even the romantic subplot(s) seems to exist just to take up space. We never see characters really wrangling with their feelings and coming to any kinds of conclusions. It just sort of gets sorted off screen without explanation or discussion.
The best I can give this is a 6 / 10, mainly for visual design (loved the look of Sidonia inside and out, and slightly less so the guardians and gauna), potential and teased ideas that never get paid off, and a few exciting battles.