1) It is explained, it even has a codex entry. It's not nonsensical, it's just a fantastical element in what is otherwise a sci-fi setting. Dune had the spice mind-melidng, ME has the Cipher. It's nicely downplayed and simply not a problem. And it is necessary for the story, sure, it's a part of it. That's an argument for the story, not against it, that it's composed of bits that are necessary to it.
The transference and process of creating the cipher isn't really explained, no. It's hand-waved. Literally, when it comes to Shiala passing it to Shepard.
2) I'll agree on a Peugeot 205 GTI T16 Rally car and a Peugeot 207. Diesel. It's a very nice analogy come to think of it, they were made by the same company, but by different people, and the newer one is generally similar (it's a hatchback), but essentially it's something completely different, it's ugly and in general a bit rubbish.
To each his own, but neither ME1 nor ME3's endings are impressive.
3) But it's there, which at least shows they thought about it. And yes, I said Vigil's file, not Vigil.
Vigil's file is an unlikely, throwaway device.
Oh, and:

That's more on-the-nose than Kaidan's optional tingling teeth.
4) Incorrect. There is no evidence, as whether a story works or not is highly subjective, and people generally didn't have your problems with ME1's story. You're finding problems where there aren't any.
I wouldn't say they're "problems", really, even if they're contrived and hand-waved. But they are examples of space magic, something you were deriding earlier as being a negative in ME3's ending. I definitely think there are hefty problems with ME2's plot that come far closer to objective observations than subjective, but that's another discussion.
5) Oh come on. The entire situation is pretty much begging for Shepard to drop by and do something awesome to solve the conflict peacefully against all odds.
Yet it still doesn't stop its origin point as an inevitable creator-created conflict.
6) Ah, you see, you couldn't be more wrong. There is no precedent. The sacrifice always has a payoff, it feels poignant but necessary (I don't know if it actually is necessary after you've analyzed the situation from a gazillion different viewpoints and come up with 13 differently written scenarios for that scene, but it doesn't feel contrived when you play it), and maybe even more significantly, there is no picking up on it whatsoever (the sacrifice thing) in ME2, where you can save everyone if you do well. Mass Effect is about earning your happy ending. I'm not having it any other way.
The sacrifice had a payoff in ME3, too: the defeat of the damn Reapers, though, yes, it comes at a price.
Just like the other endings, which weren't against the entire Reaper armada and didn't utilize the mass relays.