No analogy is perfect. Don't burn me over it

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Me? I think what they do is wrong. That doesn mean they are necessarily evil, though wiping out entire planets, sunsystems and races is hard to justify. Especially since they didn't even try to communicate (or at least didn't put enough effort into it that Humans and Vasudans were able to even notice it).
Do I need to underline the "hard to justify" part? You may be having problems getting a justification for shivan actions, but I really doubt that the shivans will be so puzzled about it. I'm not saying that the shivans aren't "evil". I'm saying that this concept of "evilness" is human. Shivans could be amazingly puzzled by this concept alone.
Notice, all this is human values, not shivan nor "alien". What is "wrong" in wiping out entire species, apart from humans not liking it? How many times you kill annoying ants crawling up the kitchen table, without a second's thought? Do you consider yourself "evil" for doing so?
Apart from the bold red part, that I wanted to bring to your attention again, there is a difference between Humans and ants. The only way I know of that Humans can "communicate" with ants is, putting down a trail of pheromons to make them go on exactly that rout.
And instead of doing so, you kill'em. You, sir, are a monster!

As Bosch showed communication between Humans and Shivans is possible.
Yes.
You won't be able to build starships and inhabit several starsystems without being an intelligent species, so the Shivans know they are fighting intelligent species.
Another human concept, one that I find extremely vague and troublesome. Are dolphins intelligent? Are elephants intelligent? Or do we say intelligence is what exists when beings talk to each other? Or make maths? Build buildings? But here we are just discussing human achievements. What do we know about the possibilities of different "intelligences" landscapes?
Why not a species that regard communication as cumbersome, stupid, innefficient, pollution?
Since they don't kill us out of ignorange, that leaves either a higher goal (the most likely one in the BP setting), profiteering or sadism/classical "the galaxy belongs to us, wipe out the lesser species" kind of alien. The latter two are just wrong, no matter how you put it.
Coz you say so? I'm extremely convinced by your argument there, "are just wrong", period. Yeah.
They could be doing something similar to what we do when we see an animal in pain and about to die, we shoot it. Perhaps they see in us only painful beings who are on the verge of self-destruct, why not spare us the misery? There could be endless possibilities, all you require is a good writer, and that's something more difficult to have

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So the only ambiguity is the "higher goal", but what goal could be worth so much bloodshed, including all the Shivans that died during the two wars?
Now notice how I ask what goal could be worth it, instead of saying no goal is worth it! Even though I think it's very unlikely, there is the possibility of them being justified or even right.
You're obsessed with this human thing called "morality". Until you drive out all these human institutions you'll begin to understand, not what the shivans are doing, but an endless and rich landscape of opportunities. I don't buy, for instance, the idea of "unintelligibility", I think it's a contradiction in itself, I think everything is intelligible, it may just be so hard to understand.
Consider, for instance, that the fact you consider X evil is exactly the reason why war between you and X is inevitable.
I dunno, we've wiped out a number of species and we don't seem too bothered about it. I can see what he's going for.
Yes we did and it is just as wrong as the Shivans wiping out species (even more so, since it's not fictional). In some cases it happened out of ignorance, when we destroyed their habitats, in other cases it was even deliberate and in yet other cases they died out for profit. And killing off a whole species for short term profit is definately evil. Even though I dislike using the word evil most of the time, here it fits.
Look, I'm not saying it isn't evil. What I AM saying is that "evil" is a human idea. It may come as a completely ridiculous one by the Shivans.