The whole Rachni thing is an example of what I mean when I say you're choices don't really carry over between games or matter in any meaningfull way.
If you kill the Rachni queen in ME1, another one shows up in ME3. Which takes all the meaning out of your decision because the entire point of that section in 1 was "do you want to wipe out an entire species or not." Sure it's easy to explain away, but all the teeth are gone from your original decision. They couldn't just have it so if you killed the queen in 1 there wouldn't be one in 2. They had to shoehorn one in so that no matter what you chose you could do that mission. So the end result is that no matter what you choose in me1, there are Rachni husks to fight in 3, and you meet a Rachni queen in 3 again.
It's like this with most of the major choices you make. If you choose to replace the council with humans in ME1 it doesn't really impact anything. The council still acts with barely hidden comptemt for you. The human council isn't bothred about human colonies being wiped out under mysterious circumstances, etc. It's all just a superficial change of a couple of throwaway lines of dialogue and some different character models. Essentially no matter what choices you make in the games, you'll see all the same things, go to the same places, and meet extremely similar characters. (With the notable exception of the boink your crew-members portion of the game I guess?)
Even the ability for characters to die doesn't really pan out meaningfully. Let Grunt die and you get a generic Krogan on mission 12 (I dunno the name of the mission lol) instead. Which would be cool if any of the stand-ins for dead characters were more than generic NPCs. It ends up feeling like the game is punishing you for various choices because most of them are binary, and pretty much identical, except generally one of the choices is worse from a writing and character standpoint. Obviously you shouldn't be "rewarded" for having characters die from a gameplay perspective, but narratively you definatly should, and this is where they fall completely flat.