I think all your choices in Mass Effect matter more than in most games. I do feel, though, that you kind of have to manipulate the plot to tell the story you want to tell.
If you're going for the Destroy Ending, there's no reason to save the Geth. Sorry, Legion/Legion VI. Control Ending means you should probably rewrite the Geth Heretics. Synthesis and Refuse endings allow for any culmination of choices, though personally I think it's a better "Refuse" story when everything just doesn't come together and the Galaxy proves it's not ready yet. And a better Synthesis ending if you end the Genophage AND save both the Quarians and the Geth.
Each choices makes sense in its own way, but I feel its tailored toward people having a certain attitude, rather than developing attachment to certain characters.
For example, you might save the Geth because you like Legion, but the Reapers? You don't meet a single Reaper who makes you fall in love with them like Legion does for the Geth. So it'd make sense to save the Geth, but destroy the reapers. But ultimately saving both Geth and Quarians trend toward the Syntehsis ending, where we see the Geth helping the Quarians despite being mortal enemies -- which foreshadows synthesis, where the Reapers help the galaxy despite being mortal enemies. But you can literally choose to destroy the Quarians (Sorry Tali!), save the Geth, and then Destroy the Reapers as well. (I'm not sure anyone chooses this). The sacrifice seems so pointless, at which point it makes a bit more sense if you choose to 'refuse'. No choice. This galaxy isn't ready. In the Refuse ending, I think your choices matter simply because it's the culmination of WHY we failed. So the next civilization can learn from Glyph where everything went wrong. I think all the endings make some sort of sense, but you kind of have to play toward the one you're going to choose.
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This isn't funny Dean, the voice says I'm almost out of minutes! ~Alexandra