Saying that writing shouldn't have political under or overtones is definitely why the 'Wow Cool Robot' meme came about. A huge POINT of writing stories is to comment on the world and express values, like that is literally how culture works, and saying 'dont write about politics' is REALLY saying 'don't raise any but the most milktoast of points.'
Part of why SR kinda got grody, at least in my opinion, was because of this shift during 4e where it hit peak post 9/11 cyberpunk. You see this really clear divide between 3e and earlier where the 'Corp Man professional runner' is this character who is despised by other runners due to being an untrustworthy sellout who wouldn't blow up some black ops torture-lab just because it was the right thing to do, to these moral robots who do things as cogs in the machine minimizing collateral damage and political aspirations. And, to be clear, this was probably unavoidable because part of SR's old thesis was 'political terrorism is justified to resist legitimate atrocities' which is.... not a message anyone in 2005 was gunna be down to have in their books. No shade at all for that happening, slight shade for being resistant to re-directing back, but eh, fictional inertia is a thing.
We are leaving that post-9/11 phase of media, and are now in the post-post-9/11 phase (which is probably not going to be its name when future media historians talk about this) and society is now not super mega-obsessed with stability and feeling invincible, which is part of why SR fans in 2015-2016 were so riotous about the ongoing tone of SR trending so cynical and passive.
Heck, SR as a RPG was one of the first 'Counter Tolkienian' RPGs. Till Shadowrun, most games, even ones with absolutely wild settings like RIFTs, treated racial moral absolutism as something that was totally normal, even though Tolkien's works were already being talked about through the lens of how absolutely racist they were in the 60's (To be clear, that isn't a 'cancel Tolkien jab, Tolkien IS a good example of a work being influenced by their time and writer), and he himself addressed how he made a mistake making all Orcs evil (To be fair, more because cosmological issues: the way evil works was the issue: The forces of evil couldn't create anything, so orcs as a pure evil servitor race rather than free willed beings didn't make sense in his universe, so good orcs were theoretically possible, and the way good worked meant that being dishonest to orcs was evil which likewise indicated that orcs have moral weight he never explored. It was never about race and he openly talked about racial pariables with the fictional peoples of middle earth). SR was one of the first settings to look at how fantasy peoples treated each other, how utterly charged the term 'fantasy race' was, and actively turn it on its head and make Orks and Trolls not marauding hordes, but an actively oppressed people. But it still dropped the ball by just sorta copy-pasting D&D concepts of Ork and Troll intellegence to them (and 1e's mixed ideas on how you should pay to be a minority standin was pretty... not great). RPGs are interesting because they lean extremely far left of mainstream media, forget most gaming cultures, yet because of Tolkien they trend towards being extremely bad on race. SR is both weirdly progressive yet also makes horrible mistakes because they code their metatypes as real world minorities to make a point (And a good one, in my opinion) but still also play into the 'they are ugly, savage, dumb, rage filled monsters' aspects of Tolkien's works.
Other things in more modern SR, however, are just plain bad writing for their own time. Like, again, no one involved in 5e shoulda thought Metatype Reduction was a good idea because it was explicitly commenting on an issue known to be a problem in its own day in... absolutely the wrong way. Likewise, the hard push for 'magical specialness' hit at a really bad time here at least in the US where the concept of being 'born better and with special powers and privleges' was NOT something that needed to be framed as an absolutely good thing, and attempts to tamp it down came across as tone deaf and very 'poor little rich boy.' Like it says something pretty terrible about your setting when if you aren't born so special that the universe itself loves you and allows you to snap your fingers for a spirit butler that you just aren't allowed to try to break your own limits via essence loss being framed as a purity discussion. It mixes so poorly with any real world non-abstract issue because body purity arguments inevitably echo into really gross weird ones. For example it frames Plan 9's method of expressing themselves through altering their body, including utilizing augmentation to express being genderfluid, as an act of 'self mutilation.' It is especially ugly when you consider the implied original plans for CFD that a freelancer implied on reddit back in 2016, made it so that Plan 9 got themselves turned into a cyber-abomination for the 'crime of doing this.' At least now they are having their day in the sun as an important character and are way less of a joke about how weird a person they would be to want to change their body a lot in a setting where... people change their body a lot. And they are even a good example of a fictionally neurodiverse character to boot (though they risk that becoming one note. Hopefully we still see some of their quirks even as they keep being a serious character).
As was said, things can get better, and the changes to Plan 9's portrayal prove it. As was noted, it was a smart idea for the astral plane to not make real commentary on your physical body and for essence loss to require deep insight and observation of an aura (it... really stinks that a lot of GMs will say a low essence aura looks 'mangled' or 'has holes' though), or for essence to not be a purity thing. A lot of people forget this, but 'Cybernetics eat your soul' was not really a thing in any foundational story to the genre, and cybernetics were actually used to talk about body policing and purity politics (because the language and politics of purity are so... fundemental to racism and prejudice, maybe its just a good idea to not posit things make you 'impure' in a cosmic sense down the line) rather than a 'loss of humanity.' Like if you read Neuromancer or GITS or watch Blade Runner and get the message 'robot parts make you less human' you... deeply failed to comprehend the intended messages of these stories. The trope of 'cybernetics eat your soul' is specifically noted to be associated with RPG tabletop gaming (mainly cyberpunk 20XX and Shadowrun) because it was an invented rationale for game balance that had the direct opposite message for how you were meant to view people altering their body and society judging them (You were meant to hate society because its super clear their partially or wholly artificial natures were not negative forces in the character's lives) and it is good that SR moved out of that lane. SR has a lot of room to move out of a lot of lanes, and to improve on its rather severe modern tone issues (Ex: Making the fact that most of the Jackpoint mages are... truly biggoted assholes who no one should like a bit more overt, and noting that magical supremacists are locked hand in hand with racial supremacists for example).
Then there are just subtle biases that come through the books. Like... SR, at least in most parts of the setting, are pro-sex, sex equal places, yet the writing often does talk about gender in Seattle through a modern lens (which is fine if that is how they want to go but its weird cuz its explicitly not the case that, for example, male orks would be arrested more than female orks in 2070 when RF was written) and its art DEFINITELY isn't gender equal: Despite it in theory being as common as women doing this, we don't get any voyeuristic art pieces of scantily clad dudes striking poses in fights. We also don't see anyone with transgressing gender expressions or an androgenous look or anything like this. This is, again, in part because of the necessity to 'de-punkify' SR post 9/11 and have everyone dress in a very unpunk way that mainstream people would still associate with punk (Again, glad that trend died with 6e and the art got way more varied and runners became more vibrant. The rigger on 54 is my fave) but... lets be fair its also because I doubt anyone holding the pursestrings for SR is inclined to ask for a sexy streetsam dude in a revealing outfit or would even know what to specifically ask for, and because its a gaming space and having the cover art for Street Spells be a pseudo-upskirt shot of a woman rather than a man, or having the person on 138 wearing a jacket open with nothing but a bra under it, is an attempt to pander with cheesecake in a way that doesn't actually make sense in SR to do. The setting (outside of areas like Japan or Aztland) don't have double standards, but the writers/artists certainly do.
Again, these are not intractable problems, and the take away shouldn't be 'give up' or 'don't try because trying gets you yelled at.' SR tried for some 20 years and because of that people ignored how bad racial mental caps were to a greater or lesser extent, it only became an 'issue' when SR basically stopped trying and became a setting that was subtly pro-eugenics, pro-body purity, anti-body autonomy.