I killed Legion in my playthrough because of the terrible Paragon/Renegade system that the original trilogy had. I was playing a neutral character, so when it came time to make a decision of Rannoch, I didn't have enough Paragon or Renegade points and was forced to choose between the Geth and the Quarians.

At first, I was pissed because it super dump that I have to sacrifice an entire species just because I didn't hand out enough compliments, or punched enough people in the face. But after some thought, I was happy with it because I'm not a fan of happy endings where everyone survives and lives happily. My Shephard's story was heroic, but also very tragic, and I love that.

I chose to save the Quarians because they are organic life that evolved through millions/hundreds of thousands of thousands of years, and to me that made them more precious. And while I like to think my Shepard would have wanted to save both, it wasn't possible in that moment and he made a tough decision. Shooting Legion down and watching him utter his last words was an emotional moment that I think made my character's story that much better. In my opinion, better than a story where everyone lives (except Legion).