(Spoiler)
Then again Emmeryn dies after chapter 9. Also consider that she's introduced in chapter 1, the objective in chapter 6 is to protect her.
Going back on Mikoto. She's indroduced on chapter 3, then killed in chapter 4.(Ouch!)
Honestly, i felt Mikotos death more painful. Why? It was pretty sudden, I felt like i was just getting to know her as a character.
Also consider the Avatar him/herself. The avatar represents ourselves. So i just saw Emm's death as like my friend's older sister dying, contrary with Mikoto It was like seeing my/kamui's long lost mother die before my/his/her eyes.
Also let's not forget that Emm's recruitable in chapter 20. and she supports with NOT Chrom, NOT Lissa, but the Avatar, and can be potentially filled with male Robin's baby batter.(Like WTFuck man! )
But hey! that's just my opinion.