Well, one thing I'd say in the writers' defense here is that this may not be an entirely hypothetical issue for humanity at some point in the future. If we ever get the point of being able to create AIs like the ones we see in Mass Effect, we're going to have to confront the question of whether they are alive and are entitled to the same rights that we have. (Personally, my own view is that if we can't agree on this ahead of time, we shouldn't create them.) So if they have a strong opinion on this question, as they apparently do, they may consider it socially irresponsible to give "equal time" to the notion that synthetics aren't alive.
True. Not to open a whole other can of worms, but they don't offer an option to bash Cortez for being gay - an exclusion which is wholly appropriate. However, if the story is supposed to be a discussion on the subject of whether synthetics are alive, let's have an actual discussion. When all the player can do is express a strawman of the position they want to take, all that does is frustrate the player. It doesn't prove the writer's point. "Show, don't tell," as they say. Objectivity is required to some degree in writing an RPG.
There are ways they could have done this. Subtle ones, not heavy-handed "does this unit have a soul" emotional manipulation. Give us the option to either hunt down EDI's body and speak face-to-face, or continue using the terminals from ME2. Between the sexbot and the Reaper code, I see them as having corrupted their own message, suggesting that the Geth weren't a valid form of life before they did something to make themselves more like us. Chris E'toile had it right - they should have been strong enough to stand on their own, to want to improve themselves instead of remake themselves to be more like organics. Railroaded anthropomorphism wasn't a good move IMO.
As I said before, my beef with the Geth is on account of their actions, which the writers did their best to sweep under the rug to make them more sympathetic. When I'm shown a third-grade propaganda slideshow where the Geth paint themselves as innocent as puppies in a war where it's been established that their opposition was almost entirely exterminated by them, that just makes them look unrepentant and manipulative.