Well, given the level of relevance that Elma's actions had to the story, I think they should go a step further and make it even more clear that she is the focus of the main story.
And yet, they should keep the avatar. The avatar is the star when it come to normal missions.
Now, how to do that? What I thought is:
Add full voice dub for the avatar during cutscenes, but decrease the amount of situations where he is given choices during the main story. I mean, most of the choices the avatar can do during the main story, have no bearing whatsoever, so just remove some of the most redundant ones. Keep only the ones where his/her choice can lead to at least some different cutscene, for instance, add one where he chose siding with Elma or Lin on you know what chapter, and make a different cutscene depending on the choice, even though the end result will still be a certain someone staying alive. So, most of the time, the avatar would speak a defined text, in situations when he/she is just making part of a dialogue, without given much of his/her opinion. Also, while the avatar should still be mandatory to story missions overall, there should be a instance where we play with Elma, without him, for instance, a brief time after chap 5 where the avatar would be in recover, because... you know why. This way, Elma will be the clear leading voice and protagonist of the story.
Now, outside of the story missions, that is, on the normal missions, and some of the affinity missions, it should remain as it is, however thanks to the avatar being voice, it would be more mass effect like. There, the avatar is the one leading the team he chose to assemble to help him/her in whatever task he needs. Just, in some of the affinity missions whose characters are very related with Elma, like Irina and Gwin, Elma would be the one in charge and she is the one that asked the avatar and the rest of the team to help out.
This way it would be more defined. A clear fixed main character for story missions and a clear mass effect style avatar for other BLADE missions. And the fact that the avatar is now fully voiced would remove that awkward feel of when he is in cutscenes.
BTW, rumors point at a direct on day 13th