(Warning! Long and rambling. For the final point, jump to the last paragraph. The rest is just explanation of the jargon I'm using.)
I think the OP's issue about suspension of disbelief vs the uncanny valley might be related to the concept of "verisimilitude". In RPGs, verisimilitude refers to the idea that decisions you make, make sense from the character's perspective in the game world. A game world that may contain cyberware, spirits, magic, etc.
For example, using a skill you've got, casting a spell, wearing armour, shooting a gun, those are things your character does and understands. But what about using Edge? Does the character choose to apply Edge to a roll? I don't think so. It's more of a meta-mechanic. It's not something inside the game world, but it's something that supports dramatic moments in play. (That's not entirely true; in Shadowrun, Edge and karma might actually be real things in the game world, just not things the character consciously controls.)
This gets back a bit to an old-fashioned distinction about different approaches to RPGs: simulationst, gamist and narrativist approaches. Simulationism is about simulating the game world in whatever detail you need, like making meatspace, magic and the matrix feel and behave differently. Gamism is about things like balance and playability, overcoming obstacles, doing the things that are core to the game and getting rewarded for that; it doesn't have to be realistic, as long as it's fun. Narrativism is about the story you're creating, and to what extent do the players have control over that beyond the choices that their character makes? This includes meta-currency like fate-points in Fate, or Edge in SR.
Obviously every RPG needs all of these to some extent; the distinction is in where you find the balance. Shadowrun has always been strongly on the simulationist end, and rather complex as a result. D&D has always been more gamist, with its levels and classes that don't really represent anything concrete in the game world. D&D4 took it further, and had abilities work in a way that was very balanced, but made little sense in the game world: you could make a special attack once a day, with no clear in-world reason you couldn't use it again. When it feels like something that should be under the control of the character, but is inexplicably limited due to balance reasons, that hurts versimilitude. You cannot do a thing that you normally can do, simply because you've done it once before on the same day. That makes no sense.
Pathfinder is also clearly guilty of that. I'll forgive D&D and Pathfinder for the way magic spells work, because, after all, it's magic. There are tons of in-world explanations that people have made up to explain that. But plenty of classes have non-magical abilities that they can still only use once a day, and that's kinda weird. Or abilities that do something that doesn't sound like the character is doing it.
An interesting counter example is Earthdawn, where classes (disciplines) and levels (circles) do represent something real in-game, and where the karma you spend to boost your chances is also a real in-game magical currency.
Anyway, to finally get back to the point: when wearing better armor doesn't improve your survivability, that hurts versimilitude. When instead, it boosts an intangible meta-game currency, that feels weird. (And if you see Edge as something magical that does exist in-game, it's even weirder.) It moves the game out of its simulationist corner towards a more abstract gamist/narrativist style of play. That's not necessarily bad (D&D has been quite successful with it), but I can understand it feels different from what people are used to from Shadowrun.
