Anybody remember writer Chris L'Etoile?

I don't think that his writing in ME1 and ME2 stands up any better than the writing done by other members of the ME1 and ME2 team and, as such, I think it's a pretty lofty assumption that his continued presence in ME3 would have made a significant difference there.  We'll never know because he left... He wasn't fired... he left.  He even worked for EA subsequent to that point, but the project he was working on didn't even get off the ground.  I do think he had problems working with the other members of the Bioware team... and I actually think his discontent would have affected ME3 negatively had he elected to stay on.

The course that ME3 took was set in ME1.  The ending was even clearly foreshadowed in ME1.  The direction Legion's character took was set in ME2.  The presentation of the geth who worshiped Sovereign like "heretics" was actually set up in ME1 with the little sequence about the glowing orb and Saren's reference to Sovereign being insulted by the petty devotions the geth hurl at it.  There is NOTHING in his dialogue in ME3 that materially changes his personality from that presented in ME2.  He still talks in exact terms, still continues to point out how what he's thinking differs from what the humans say he's thinking.  Even his statement about being no better than humans is framed within a context of compiled data.  I simply fail to see any sort of dramatic slide in the writing quality over the course of the Trilogy.  It's all written at about the same Grade 9 level (and that probably intentionally caters to Bioware's target audience).

Are you serious? If anything can be clearly recognized from the various elements of those two games, it's that the ME team didn't have the slightest idea where things would end when they made the end of ME1.

As for Legion and the geth, the difference is that in ME2, the geth were eventually recognized as a valid form of life in their own right, while in ME3, they needed an additional pseudo-numinous something that by nature only organics were supposed to have, and which was supplied - in an irony that I'm sure escaped most players - by the Reapers, as a stand-in for the transcendent, and the result was that the geth acquired human-like individuality. Again, a prime example of making humanity the measure of the universe, as opposed to ME2.

The Hanar culture was also highly dualistic, what with their entirely separate face and soul names and referring to themselves as the impersonal "it" or "this one" when dealing with strangers and passing acquaintances. Their culture is also built upon the notion of extreme politeness; even in the face of those they hated. The religious overtones were an obvious parallel to humanity, but aside from that one instance with the zealot in the Presidium the Hanar were actually quite distinct from normal human interactions.  

Same thing with the Elcor, all of their slow, deliberate speech and added descriptors before statements was because of their extremely subtle body language and inflection of tone. They literally spoke that way for species like us humans' benefit. You could almost say that humans were too stupid to pick up on the minute details of an Elcor's communication; "an interaction among themselves of scent, extremely slight body movements, and subvocalized infrasound to convey shades of meaning that make a human smile seem as subtle as a fireworks display"; so they had to slow down and practically spell everything out. The fact that two of them were talking about the consort doesn't detract from their 'alien' qualities, just that they are capable of communicating along lines that we could find familiar. 

Rachni are the same way.

All three of these species weren't needlessly esoteric (like the Reapers) just for the sake of being otherworldly but they did have distinct qualities and traits that set them apart from the norm. All the other species: the Asari, the Krogan, the Turians, the Salarians, etc. you could replace all of them with a human and nothing about your interaction with them changes. You couldn't do that with these three outliers. The fact that they had non-human appearances was just an added bonus on top of rather under-appreciated writing.

Do you think it would be possible to create an alien that is truly alien without obvious parallels between them and humanity?

It is probably very difficult, if not impossible, to create a character you can interact with without any human aspects, but that's not necessary. In order to approximate an alien mindset, you can enhance certain human traits and downplay or remove others. I think Bioware successfully went a little in this direction two times: with Cole in DAI and - ironically - with David Archer in ME3. Of course, neither instance was SF (David Archer was IN an SF story, but he didn't represent an SF concept), but SF stories using "structurally unusual human minds" as an "alien" theme have been created. C S Friedman's "This Alien Shore" is one of the best works of SF I know.

The above condition also leaves a loophole that has also been used in SF: The "The Red" trilogy by Linda Nagata features an AI that never loses its alienness because nobody has ever found out how to directly communicate with it.

You can also showcase an alien mindset by giving your alien mind priorities and decisions that, while the writer may be able to imagine them, a human would never actually have or make. ME3's Catalyst had great potential in this regard, and I've always argued it is not insane, shackled to a faulty programmer's code or suchlike, as many people argue, but simply had completely non-human priorities and a completely pragmatic attitude. Had the games not pushed the horror up to eleven, suggesting "gross gratuitous evil" rather than the required clinical detachment, and had we been allowed to explore the Catalyst's priorities in some depth, with dialogue on both sides that made sense, it might even have worked.

Finally, there are ways to express a character's alienness in spite of eventually establishing understandable communication: In E William Brown's "Perilous Waif" the protagonist, Alice Long, attempts to communicate with an AI, but she can only do it because she has a highly-enhanced computer implant thoroughly integrated with her brain, and after exchanging mathematical concepts for a while to establish a framework.

So yes, I think SF can approximate alien mindsets, at least enough to deal with them, and that which makes them alien, or that which enables communication in spite of it, in some depth.
 
In addition, we were not just talking about alien characters, but about ideas and technologies. In the "Corporation Wars" trilogy by Ken MacLeod, reconstructed human minds live within a simulation long after their originals died, and we see, for instance, a character reflecting on the fact that it's not economical to run all parts of a simulation all the time if there's no one to experience it. Also parts of his life in the simulation have never been actually experienced by anyone, even though he remembers having experienced them. Nonetheless, he experiences his life as meaningful. It is a setup alien enough that thinking about it too deeply could drive people to insanity.

What Chris L'Etoile actually suggests in one of his old posts is that the decision to have things go into a direction he didn't like - I think he said making Legion less alien was one of those things - was made by a person above his paygrade. Also I know that Patrick Weekes can be very good at writing unusual characters, though I also think he's better at the emotional stuff and not really very good at exploring SF themes*. So the question I'd ask is "why was that  decision made" (since I consider it almost anathema to the genre)? If itwas made to make Legion more "relatable" (I came to hate that word), I'd say they failed in my case. For me Legion represented the geth distributed consciousness as described in ME2, and I found that way more interesting than the AIs with standard human-like individuality that ME3 thought we should value just because it's more human-like. Bullshit.

This is also related to the other accusation I often level at ME: that their writers, all too often, didn't think things through in their worldbuilding. By Legion having been written this way in ME2, I can infer that some thought was put into it, and I value that. The parts of the MET I recall most fondly are when SF themes are actually explored, at least a little, rather than simply used as plot devices. Another little example: the exchange between Adams and Chakwas about synthetic life, with Adams asserting "we're all machines" while Chakwas asserting there was something more about organic life.

*I recommend his (non-DA) fantasy books. The style is not my favorite - too much over-the-top-ness - but that's just preference. They're quite good. 

How was legion made less alien? 

ME2  directly shows the Geth can have different and individual mentalities. That is the only reason why the Heretics even work.  A certain portion of the Geth willingly decided their action was the correct one to follow a Reaper.  Legion even explicitly tells you that. The Heretics were not hacked or reprogrammed they decided by their own choice to separate and the True Geth let them go. Not to mention Legion and his over 1k Geth programs were separated from the Geth Collective for months if not years depending on when he left to find Shepard. Different experiences that are not shared among the collective will alter Legion's personal outlooks and mentalities while other Geth remain different.  Once reintegrated into the Geth Collective it's unique memories and experiences would undoubtedly cause an effect and change the perspective and actions of the rest of the Geth.

They already had individuality the only difference is they are able to share memories in a way that we can't even begin to comprehend. Communicating at speeds organic life is incapable of. With out the short comings of pride, ego or emotions to get in the way of rational discussions. So it appears they are rather monolithic mentality only because of how they exist. The change of them into fully realized AI with a more defined sense of self because they are no longer so interdependent on each other didn't change anything about them other then improve them. 

On top of that their massive interdependence on each other to achieve any form of intelligence or sentence is a strength and terrible weakness at the same time. A weakness the Quarians exploited then the Reapers exploited to destroy/enslave them.  The only way they would survive the Reaper invasion would be to remove that weakness and the Reaper code upgrade is the only way. Now they are no longer so interdependent on each other for intelligence and can operate as individual freeing them of that weakness they suffer while still allowing for their strengths as a unified mind that is capable of communicating with each other near the speed of light, sharing memories and facts allowing them act almost as one being.

Complaints like this seem to miss context. The context of how the Geth operate or at least how we are told they operate, and the context of the change and reasons for it.

Him not being there for ME2 is probably the main reason they screwed over the Virmire companions. He did a great job with Ashley in ME1 and in ME2 she got next to nothing.
Although writers probably don't have that much influence in deciding what happens in the grande scheme of things. I doubt if he were around for ME2 it would have changed much as far as the fate of the Virmire survivors goes. They really wanted to shift the focus towards the new companions in ME2.

I guess its more of a catch 22 in that sense.

Either he leaves because he disagrees with the prevailing vision of the project, and is decried as someone who doesn't work well with others. Or he stays and has his work, focused on maintaining a consistent, believable universe, changed by higher ups, who are increasingly abandoning the franchise's science fiction foundations in favor of the 'Rule of Cool' and characters before plot mentality.

I feel the same. And I don't view Mac Walters as a bad writer, per say, but I do feel that he isn't a good choice for being lead writer. He is a good character writer, but without any real oversight to reign him in, it's hurt the series overall (IMO).

Case in point being his unabashedly favorable treatment towards Cerberus. Forget Liara being the franchise writer's pet, it's Cerberus that takes home that prize.

Going from forgettable d-plot villains and mad scientists in ME 1. To an ultra-secret black ops splinter group; with more money than several other species; that players have to work with in ME 2. To becoming the Sith Empire; with fleets on par with other species' militaries; and then somehow being more concerning to the Reapers than the rest of the allied forces; despite obviously being indoctrinated; in ME 3. To finally getting their own establishment in ME:A and the implication that they will be a major player in any forthcoming sequels. 

Cerberus was Mac's baby and the amount of attention it received over the course of the the last two thirds of the original trilogy really didn't do any favors to the rest of the game (again IMO).