Super late to the discussion about characters, but I've been on a travel course so that's my excuse.
It's close between her and Yakone, but Atka. Across all the collaborative writing I've done, few characters have surprised me as much as her. When I came to this site, I felt as though I were standing on the shoulders of giants. I wanted to contribute something unique, but I also didn't want to make too much of myself. It's easy to forget for anyone who remembers who Atka became to everyone, but I intended her to be a supporting character. I had thought "someone else will emerge as a central protagonist."
And, much to my surprise, my Guardian Spirit became something more. The Scarlet arc unexpectedly thrust Atka into a position of importance. She helped Commander O'Brien, gained her trust and an early leadership position - and the rest is history. Atka grew in strength and skill as a psionic warrior and developed as a character, gradually shedding past guilt and an insular personality to become an icon to XCOM. She had such significance that I couldn't not include her in LoE, and she'd surprised me with such depth in SoD that I knew I could show another side of her character - how she might change if pushed to despair.
Bringing her back from that darkness constituted a beautiful arc and a wonderful send-off for the character as she learned to be a leader and a mother again, as she had in the SoD timeline. So yeah, while I love how planned and executed Yakone's arc was, I've done so much with Atka that she holds a special place in my heart and memories. And I know from experience she left an impression on you guys as well.