That would've been a great ending, I agree, but it would've just stopped the whole story in its tracks. Let me put it this way - Kerrigan was way too powerful. But they obviously have no intention of keeping her as the main villain, which makes sense - new game, new primary villain. Okay, it doesn't really make that much sense, there was still lots of room to develop the existing characters, but the point is they wanted a new villain. In order for this villain to be actually threatening, we can't have another uber powerful villain running around. Okay, maybe we can, but then the story would be completely GRIMDARK. Basically all the good guys would be able to do is to sit on their asses and wait to see which one of the big bads will win the grand prize of eradicating all other life in the galaxy.
It COULD potentially work out alright in a pseudo-lovecraftian way, but Starcraft's never been that kind of game, in all of Blizzard's stories there is always at least some light in the end of the tunnel. In what you're saying the light at the end of the tunnel isn't even a train, it's the lights from two marines' armors, who are impaled on the rapidly approaching tusks of a Brutalisk.





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