The bugs can't be that threatening because an entire Virtue tree is dedicated to hunting them down Starship Trooper style. Even farming them. If you amped up the bugs, you'd need to amp up that Virtue tree as well, and it throws the Virtue balance into question.
I do not think CivBE's portrayal of alien life as conquerable is a design error. The Xenodome, in fact, is a Wonder aimed at preserving and displaying local life in its natural habitat - a clear indication that humanity eventually gains near-total mastery of the alien ecosystem. The design reflects the planned narrative. It is a more logical and thought-out progression that SMAC's "suddenly we contact Planet and we become one!" which makes about as much sense as cave people suddenly gaining insight into how to make a bicycle.
Gaining understanding and more and more mastery over local ecosystems is what eventually leads to communion with Planet, not an unexplained sudden super-thing.
I thought that all the praising SAMC how "artistic" or "masterful" it was was the worst part of this thread, but this comment is wrong in so many ways.
First, there is no "Virtue tree dedicated to hunting them down Starship Trooper style". Might has two virtues giving bonuses for killing aliens. Two virtues out of fifteen. That's entire 13 % dedication. That is like talking about someone who has a wife and six mistresses as "dedicated husband" - Even worse due to rounding.
And the pseudoargument with the precarious balance of Virtues thrown into question is just that - a pseudoargument suggesting that Virtues atm are balanced and any change in the game would set them into some disequilibrium that would be painstakingly hard to balance.
But what is borderline outraging lie is the rest of your post. Gaining understanding and more and more mastery over local ecosystems is indeed what eventually leads to communion with Planet, and that what is SMAC all about. The flavor text are from the beginning talking about studying the ecology of the planet, the unease resulting from the realization that ecosystem of the Planet looks managed, the research into psi phenomena, first contact with the planetmind, research into the planet growth cycle and then the "Communion" as an effort to break this cycle. No unexplained sudden super-thing at all.
In fact, it is the presentation of this story that outclasses BE by leagues. In SMAC, there is some story told over all the tech quotes, building flavour texts and tech description. But it always in background, never going into needless details that would only bore and distract. Heck, if something is "masterful" in SMAC it is its ability to tell a narrative without telling some particular story with a set of cross-referencing texts. SMAC gave me an appreciation for all the postmodernist stuff that I've begun to read some years after.
In fact is is the importance given to specific stories and needless details that is killing the immersion in BE, imo. There are many stories about some specific battles where Wonder proved its worth or by technical descriptions how it could work. Yeah, in SMAC there were two or three quotes dedicated to some war between Sparta and the Gainas. But they were brief and illustrated the Project/tech/building sufficiently. In BE I can read about the one battle Markov Eclipse was used (Great inspiration for a wonder, through. Together with the deep thought my favorite) which could be ditched altogether, it only confuses me when I want to read what the heck did I just build.
What I really miss in the flavor is feeling how they are on a new planet and represent maybe the last what is left of humanity. SMAC used some of its flavor to describe the difficulties of establishing industrial and logistic chains in similar scope that existed in Earth. In BE I don't have a feeling that they managed to land on some distant planet at all.
And it is not because we "don't get it". I think that we (or at least I) do get the visions of technological marvel that the authors of BE wanted to show us. I am just not interested. The technologies described are not that original, i read similar concepts before, and they are just that - technologies. Somebody in this thread already wrote that SMAC is talking about people, people on alien planet or the impact of future technologies on people. And that is what i am in good sci-fi interested in - people, not technologies, because i am (still) human.