There is your problem.
The inherent problem of writing an alien is the writers and the audience are human.
This.
It is also a technical issue.
You need to design many of the alien species to have a humanoid shape so that they can function as squadmates in the gameplay portions. Truly alien species, like the Hanar or Elcor for example, would need a lot of extra work to make them function as squadmates compared to those who can share the same animations as human characters, like the Asari or Quarians.
That isn't to say that the series can't introduce some more alien species that are very alien in appearance, but they're never going to be a majority, and it would be slightly unfair to criticize the devs for having humanoid aliens considering all the extra work, time, and money that would need to go into making every alien unique and function differently from humans.
Humanoid aliens also may not be as far-fetched as some imagine. Convergent evolution could produce something that is at least broadly similar to us. They wouldn't look exactly like us, but bipeds with two arms and hands and a head with two eyes, a nose, and a mouth in the same place as ours...it is certainly possible.
The only species whose appearance ever bothered me in the series was the Quarians, after Tali's reveal. I thought they were the one species that veered too closely to humans. Even the Asari, who are very human-like, appear alien compared to the Quarians.