I've handled one and don't like the following
Granted my experience is not having handled one once, rather I've owned half a dozen of them, and shot thousands of rounds through them, but I see your complaints as none issues.
They're finicky about ammo, and the gas system only has two settings. You have to know what you're running, and if it'll be to heavy for the setting you're on. In mixed ammo situations you could &!$@ yourself in a hurry.
First I would disagree that they are finicky with ammo. They as a general rule don't like Winchester Bulk ammo that one finds at WM but I've seen lots of guns fail to eject that crap including 870s. Every other ammo (I don't ever buy the winchester anyhow for any of my shotguns because the Federal is better quality and the same price) I've run through mine has functioned just fine.
Second the gas system is not an issue. You aren't (at least I hope not for your sake) going to use bird shot period in a defensive situation or keep a defense gun stocked with birdshot. There is even less reason to be switching between light bird shot target loads and buck/slugs. I'd be more worried about the bird shot in a defensive situation than the gas system. Even if it somehow became an issue I would not spend any time worrying about having just &!$@ myself. I would simply reach under the gun and quickly work the charging handle until I was in a position (i.e. behind cover) to flip the setting. Yes it is slower than the gun running right and a bit slower than a pump but it is not that slow. I actually saw someone run a three gun course that way and they beat a number of the pump gun times (based on reloading speed mostly).
The box mags also don't handle 2 3/4 gracefully.
Honestly I'm not sure what that is supposed to even mean. Furthermore, there are a number of different makes of saiga box mags are you referring to a specific mag or all of them. I only own 20+ mags (a mix of AGPS, AGPs modified for a magwell, factory mags, and a MD drum), I have never had an issue with 2 3/4 shells. I've shot thousands of them, bird shot, buckshot, and slugs. In fact they are what I shoot 99% (or more) of the time. Gracefully is a vague adjective but I serious don't know what issues you could be eluding to.
Sight radius is too short. Needs an AK style front sight, not that gasblock thing.
Assuming that one really needs to change it this is a rather cheap and easy thing to change. e.g.:
If one is not up to adding a front sight then the S12 is probably not the gun for them.
The buttstock is hollow and noisy
People leave those one the gun???? Most owners scrap the stock but it is for a myriad of reasons more important than the fact that it is hollow. Some people that inexplicable keep the factory stock fill it with foam, which is pretty dang cheap and easy.
The S12 has it warts and there are some pretty legit critiques IMO that need addressing and or make it a gun some people would want to pass on but none of them are the things you listed. Of course it probably takes more than "handling" (what ever that actually entailed) one to know what they are.