Giving spirits a weakness is the key then really doesn't matter how op they are. i think of like superman needs krytponite to be interesting.
The best Superman stories tend to not feature kryptonite at all or use it extremely sparingly. When writers lean too hard on kryptonite it generally is a tell they aren't really writing the Superman character.
This goes doubly in RPGs, most editions of the D&D DMG for example heavily warn away against constantly nullifying player power because its a feels bad moment where the thing you were promised would be cool and fun isn't working and its not realistic for a player character to respec to deal with the problem. The classic "Fire Sorcerer not having fun because you keep throwing fire immune enemies at em" or "Taking the decker's deck away to 'challenge' them but they just mope unless the removal is extremely short term because suddenly everything their PC was about was poofed away" problem. Luckily, spirits for both PCs and NPCs don't really have that issue.
I would say, however, that a key fix to Spirits needs to be 'build agnostic.' It is totally, 100% fine if different archetypes have different ways of handling a problem and some are more direct and efficient than others, but the response to the question "How do I interact with a bit of the shadowrun world and overcome challenges related to it" should never be "Be an entirely different type of PC."
That is why a viable solution to the problem should be weapon, power source, and build agnostic: You shouldn't be out of luck because you didn't take killing hands, rolled mundane, or use bows or guns or melee. Its fine if it isn't fair for NPCs (in fact its ideal that NPCs can't casually have a plan for dealing with spirits in their back pocket in the same way runners can) but spirits are too big a part of how corporations deter shadowrunners to make the answer "Get a mage or adept to deal with it" acceptable.
As for Genie Logic, it strikes me as a poor substitute for actually balancing the spirit, similar to how background counts didn't really balance mages they were just a shrug to the GM telling them to arbitrarily penalize their mages and adepts till they felt it was alright in a way that wildly varied in actual outcome and targeted 'honest' uses of the abilities in question more than dishonest one. Genie Logic just encourages you to use spirits in simple, powerful ways, which often are the ways that sorta make other archetypes feel redundant and steal their spotlight (Especially samurai) rather than in nifty cool 'magey' ways. It also encourages very legalistic spirit services that are likely to slow the game down, and if a player is more casual about it they may feel 'gotcha'd' for using an iconic mage power that SHOULD be strong.
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One thing I have been sorta toying with for 6e is to make it so EVERY attack vs a spirit that is nullified by ITNW generates an edge (ignoring the edge limit), every offensive/negative spirit power you are subjected to generate an edge, and every attack a spirit makes against you that fails to hit or kill you generate an edge, and make an edge action (probably 5, but maybe 4) that allows you to make an attack against a spirit that ignores its ITNW and defense action. And, if a spirit a mage has summoned is banished or disrupted, that summoning 'slot' becomes locked for a bit to prevent just spamming spirits.
The outcomes of this are interesting. Thematically, it sorta makes sense that spirits would be suddenly vulnerable to a combatant determined enough to fight them for a few passes and for lucky/fateful shots to hurt them. It evokes Neijia a bit but is more general, free to all, and less, frankly, bad.
Mechanically this encourages PC mages to not casually try to throw spirits at problems unless they are a really good fit, because if you toss a spirit at a bunch of mooks your generating edge for those mooks faster than the spirit is likely to kill them. Combat PCs still want to do stuff like target weaknesses of NPC spirits or the mage summoning them, but if they absolutely have to fight the spirit (Ex: The mage is an offsite mage, or they are bugs bugs bugs) they are still rewarded for their investments into combat even if the fight is way harder.
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Also, more tools and things that interact with spirits in a more nuanced way help. In 5e the mundane usable anti-spirit options were 'spooky overpowered bioweapons that cost a ton' or 'niche expensive thing like a magic horn that is likely to not work anyway.' It just didn't work to make 'Only ones able to fight spirits' part of the mage and adept Pie because it meant any tool that was there to help mundanes deal with it felt like it needed to be pretty much unusable to justify more specialized anti-spirit stuff that mages and adepts had that was STILL bad because the best solution to spirits was throwing your own spirit at them.
All 6e really needs to do is print ghostbusters tech and things would be good to go. Like as simple as "Hey this thing turns ITNW into a mere soak bonus when turned on but it isn't a grenade so it needs to be placed on the ground and it shorts out after a minute" sorta stuff.
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For the game as is, and honestly even after spirits get balance changes, SR is a game where secretly there isn't a major street-prime distinction, your either a total chump or you have resources, and the game goes out of its way to be really unfair to total chumps. It is why the street level rules have never really felt good in SR: SR as a system isn't set up to ensure granularity of result among unauged characters with middling skill values and little access to equipment, because the game is about mages, street samurai, riggers, ect who decidedly are not those types of characters, and even PCs who evoke them are so out of their league that the trick to playing a PC who feels like they were a ganger is more in framing than actual mechanical power level. The mechanical difference between a ganger with 2 skill and 2 attribute and a corpsec with 4 skill and 4 attribute may as well not exist for anyone besides maybe the face and decker as they both generally miss in combat and have no way to handle any sort of superhuman combatant like a spirit or street samurai without highly specialized tools.
If a gang doesn't have an awakened member to its name, it is one of those tiny neighborhood gangs that tends to get swallowed up when a major player like The Ancients, a Go-Gang that is essentially a puppet of a hostile foriegn power which regularly funnels things like machine guns and rocket launchers into the Seattle black markets and which can start street wars to casually remove zone ratings from an area in defiance of KE as they refuse to be dislodged, decides to glance their way and have one of their mages start assaulting them with scry and die spirits. That neighborhood gang just... legitimately can't resist any group able to leverage any 'new' resource of the 6th world against it, remember this is a setting where a street gang if it wanted to spend the money could drone strike a building. Cruddy, scrappy gangs armed with sport rifles, pipes, and dreams exist, its just that most gangs who PCs have reason to care about can bring deckers, pseudo-samurai, riggers, and mages to bear, even if they are extremely weak by PC standards. The guys fighting for scraps are regularly just annihilated by anyone, even a somewhat fighty Face who invested in a little combat 'ware can hold their own being ambushed in an alleyway by those guys, a high force spirit is overkill.
Most groups of course can't have anti-magic sitting everywhere, so the way you deal with a hostile spirit if your one of the unlucky people who's job it is to delay superhuman combatants until HTR or backup or whatever arrives, is going to depend on your organization, its resources, and what you got. A gang may just call for Magic Larry to send as strong a spirit as he can, and if Magic Larry's spirit loses, that gang is going to bug out of that fight. Corpsec may try to send drones to sweep for unidentified people to try to neutralize any mages, use suppressing fire on the spirit to try to contain it, or utilize some on site 'ace in the hole' to help hold the line like drones with rifles or warded panic rooms to hold their VIPs in. The Ancients, if they don't have a mage or adept in the area, may just fall back if one of their 'officers' are there, or if they are a more... motley bunch in the middle of a 'turf war' with the government just start firing heavy weapons and explosives into an area because those fraggers are crazy.
