The problem here is not that the Matrix is a negative mechanic in Shadowrun, but that the underlying idea/mechanics that reify threat in Shadowrun don't lend themselves to any sort of shared investment. And that is a direct result of too much mechanization, not just in Matrix experience but in the system as a whole.
I say that as someone who has played Shadowrun since first edition, with all the scars, bumps, and bruises that implies.
The Matrix/abstract computational environment is a required trope and cyberpunk literature. You can't get around not having it or talking about it and still maintain your position in creating that kind of narrative. It's got to be there. Because Shadowrun is effectively a cyberpunk pastiche, it has to have cyberspace, one way or another.
This creates a clearer narrative niche: the hacker has a place in every story because the stories are grounded in an extant genre of literature with fine examples. We, as the audience, know how the hacker is supposed to fit into stories because we have seen how they have fit in the stories in the past.
Shadowrun's problem is that the mechanics are set up so that the Matrix just has too much going on. Mages have much the same problem if they intend to astrally project and provide support spell craft – in fact, very much literally the same problem if you go by the text. The GM is handed a pile of issues and an entirely different perceptual universe for that character to interact with and deal with threats from, and expected to balance the whole narrative. It can be done, but it requires some juggling.
To do it well, you have to pace the threats being experienced by every player at the table at roughly the same time. The mechanics around the Matrix aren't all that much different from the mechanics around the guys sneaking through the hallways, and if you're doing it right they should be hitting difficulties at around the same time looking to solve the same problems.
Shadowrun doesn't help you a lot here, but very few games do. It's not a matter of specific mechanics so much as a matter of too many mechanics in general to deal with.
Consider how Wushu deals with cyberspace: since all of the exponential mechanics in the game are abstracted to the same level, and the results of failure are directly mechanized but abstracted, your hacker doesn't have to be standing in the hallway with the cybered up samurai to be engaged meaningfully and threatened meaningfully at the same time. The Threat (a mechanical representation of what needs to be overcome in the Scene to proceed) affects everyone, whether they are leaping across the hallway firing an Uzi in each hand or sitting out in the van slapping at keys and trying to break the ICE keeping them from unlocking that blast door. Successes decrease the Threat, failures decrease character Chi, and it's the same for everyone. (In fact, they can also be the awesome, near supernatural sniper perched on top of the next building and still involved in the current conflict.)
The problem is not a specific set of negative mechanics, the problem is that the system in general doesn't support a coherent narrative experience.
It's difficult to suggest a particular mechanic or subsystem or minigame "doesn't further the course of play and storytelling," because different groups and different GMs have different acceptable cognitive loads, have entirely different play styles, and want different kinds of storytelling. If you are good at and enjoy the kind of storytelling that rapidly jumps between different locations/contexts, Shadowrun's Matrix mechanics may work just fine for you. If you're not, or you don't, then they won't.
Overall, it tends to be more useful line of analysis for me to look at whether or not the mechanics as a whole are getting in the way of the play that I want to have rather than an individual mechanic. That's not to say that individual mechanics can't be bad, but it's not necessarily as clear cut.
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I actually think that the matrix in Shadowrun is amazing.
It just doesn't add to the larger game. A negative mechanic can be tremendously clever, but it just detracts from the game. A positive mechanic would be something like D&D 5e's advantage mechanic: it's a really cool way to give flavor and is super-simple to execute, so if you aren't opposed to it for some reason it's a really nice addition to a system that is pretty simple.
The problem with the matrix is that it doesn't just adapt a trope into the game, it does so in a way that makes a whole separate game within a game.
Regarding the notion of the matrix versus astral projection there's a little bit of a false correlation there; the astrally projecting magician definitely sees different things, but they're still fundamentally in meat-space. The matrix often has a connection that way (especially in installations where the matrix is embodied by a physical representation of that space), but data-runs, for instance, are going to almost always take the matrix people to an entirely isolated sphere, while a projecting mage is at least in an overlay of reality.
It's probably fair to say that some of this is a problem with Shadowrun, but it's a problem that comes from a design philosophy that is willing to accept a certain amount of fragmentation and then jumps in wholesale.
I will agree that it's possible for some groups to have a good time with Shadowrun's matrix mechanic, but it's also been something that's definitely proven to be negative more often than positive; as a game designer you want to look at the average, not the exception, and the problem is that Shadowrun doesn't have a system for the average roleplayer; it has a particularly math-heavy game.
For early Shadowrun, where there was much less user-friendliness in many ways (at least, less of an attempt at such) than in 5e, this was fine (I also think that there was some rules elegance that got lost over the years, but that's for a later date). Each character had their own nuanced elements, though deckers were almost always the most difficult in my opinion (barring really weird exotic builds).
The real issue is that you have a game that has some interesting design decisions, but which has become too clunky and bulky. A decker doesn't enjoy a separate ruleset, they use the full ruleset and then a superset (or, often as many as three supersets, since they will have cyberware and sometimes rigging), and requires the GM to do so as well. Compare this to a magician, who might also have a couple supersets (e.g. spellcasting, summoning, and projection), but will often share those duties with other characters because, unlike a decker, the other supersets don't represent a way to recover sunk costs but rather another path to excellence.
As a designer, what I'm always looking at is when there's a part of a game that reflects a problem within the philosophy or design structure. That doesn't mean that any part of the game is necessarily bad in its own right, but it could be something onerous. To use another FASA-affiliated game, the Battletech roleplaying game has life-path creation systems (and only life-path creation systems) in the Time of War reboot that my players just couldn't sort out. It's a fantastic system once you get to play, but if you don't have a lot of buy-in it just becomes a problem that players don't want to deal with.