yes Bioware is responsible for the changes to both the Mass Effect series & the Dragon Age series but Bioware is part of EA now. So anything that hurts Bioware hurts EA, so with Mass Effect 3 getting such bad press is going to hurt EA more than Bioware because Biowaree is EA these day's.
All the development cost's are paid by EA, so with the ending to ME3 having such a negative impact on the fans they will suffer for it.
I wouldn't bank on them listening though, they never listen to the fan's when it came to DA so why would they bother now. They've made it more than clear that they would rather abandon the RPG road for the action/FPS road. That more than likely being EA's influance as all EA thinks about is money & action/FPS games sell more than RPG's.