As for magic, fantasy has its type of magic and Sci_Fi has theirs. But it's still magic. There should be no way you can go FTL so they create magic to allow it. Instant communications may have a small link to quantum mechanics but it's still magic. The big difference in fantasy vs Sci_Fi is that somethings we think are magic may in fact be possible with future discoveries. But that might apply to a wizard using telekinesis. Star Wars has it's force which is big space magic but maybe someday we can contact the dead and get power from them.
My point is very simple. Sci-Fi by definition must have space magic. In many 4x space games you can win a victory with transcendence where humans evolve into a super being overnight. Sort of like humans in Star Trek becoming Q. The whole synergy thing is not new to ME and it's a vehicle used in many books, movies and previous games.
True. For examlpe, of course the part with "quantum entanglement communicators" directly contradicts quantum field theory, which unifies quantum mechanics with special relativity to account for the speed of light as the maximum speed at which information can be transported. That's not the problem. The problem is, that once the world is in place, you should not break your own rules, especially not in the ending, and especially not to achieve resolution to your main conflict. That's what the ME:3 ending does.
From a storytelling perspective, I think your comparison to the "Lord of the Rings" is apt. Two thoughts:
Death of the protagonist:
If the writer made Frodo die on Mount Doom, would people hate the ending for it? I wouldn't, if there is a good reason for it. Telling the audience "See, I don't do simple servile wish fullfillment aka HEA", does not count as one. There is a point in letting him live: We see him suffer, traumatized, unable to reintegrate into society, which is contrasted by Sam. This connects to a deeper human theme that many of Tolkien's readers who lived through WWII could connect to (we can, too, I think). That is why it is a better idea to let him survive instead of killing him of.
Magic:
Gandalf could fly to Mount Doom, defeat Sauron and destroy the ring by his magic. That's what the ME:3 ending does, to a certain extend. Tolkien has very carefully established that this is not possible, without giving away much about what Gandalf really is, and what he can do. Tolkien also gets away with resurrecting Gandalf because that is not used to resolve the central conflict at the end of the story. Magic actually has a very minor role in the plot, it certainly is not used much to solve the problems that the story throws at the protagonists.
80 - 20 rule. It applies to probably around 80%. Only the individual being completely honest with themselves knows for sure.
The 80 - 20 rule may or may not be true (how do you know?), but this thread is obviously a discussion between individuals who are not a representative random sample from all ME:3 players. Judging by their contributions to this thread, they all belong to your 20% quantile.
I think we get the most interesting discussion by responding to what people actually say, not by responding to what we think they would say if they were completely honest with themselves. A remote diagnosis in the realm of depth psychology is bound to fail on many levels, even if one has mastered quantum entangled communication. 