Keep in mind that the goals of a nice fictional book are not at all the same as of an academic paper or a thesis. The former is primarily about entertaining or stimulating the reader. The latter is about providing a certain information (the research result) in the clearest way possible.
The "many things one can do to make the text better" that you mention are geared towards making the text easier to read and less of a chore. While this is certainly also valuable for an academic text, being "easy to read" is ultimately a nice-to-have, while clarity and non-ambiguity are absolutely essential. If you keep in mind that clarity absolutely should not be compromised, you will get an impression why academic texts are written the way they are:
As you say yourself - if you strive for clearness, having multiple names for the same thing is not good at all.
avoiding passive voice
Academic texts tend to prefer passive voice mostly because the "story" of an academic paper isn't about the writer, it is about the effect that is observed / described. Writing the paper like you are telling your mother what you did the lest 5 years would put the emphasis on you and your experiments, rather than the data and the observed effects.
breaking down long and complicated sentences
Yes, do that. Even in academic texts. It's just not easy for those of us that don't have English as first language. In German, for instance, you are taught from very early age on that short sentences "sound stupid". This is hard to unlearn.
letting the reader to think for themselves
You will never want to "let the reader think for himself" in a paper. It's not a piece of art. You want to present the facts and what derives from them as clearly as possible, not write your paper in a fluffy way so that every reader can come to the conclusions that are most suitable to her/him.