Shotguns should not be put in with Automatics, no matter what you name it. Shotguns are a utility weapon, and should be made more so - and one of the balancing points of Automatics needs to be that it lacks that level of direct utility.
In any case: Having too many weapon skills means that the balancing method inevitably shifts towards everything being the same, because there's only so many ways you can differentiate. It's a delicate trade-off, and the weapon system as it stands can only support a fairly small number of skills. Just making Firearms the skill, frankly, has a bit of the same problem - along with the loss of character customization; this would also be a bad thing.
Moving Machine Pistols out of Automatics, however, risks taking away the idea of Automatics having an option for every situation - the skill should have broad uses, but lack deep utility to contrast against the more specialized Pistols and Longarms skills.
And no, you simply cannot have game design and simulationism share top priority - there are differing concerns at play and many times that the right choice for one is the wrong choice for the other. Game design is all about trade-offs, and in some cases that trade-off will be "option A is more realistic, but option B (increases agency/improves balance/offers more customization/<insert any other of the myriad game-focused concerns here>)".
Splitting based on range would have... Issues. Many of them. Including the fact that it would just feel wrong to some players that they have to use a different skill to fire the same weapon. And, frankly, this seems like a case of harming realism for a very dubious gain, especially when there are other, better ways to deal with it.
In truth, the existing weapon skills that far off being balanced - a major overhaul is not needed.
yeah what i actually said in my post was "rename automatics to ASSAULT WEAPONS"
shotguns=close range assault weapons and therefore suit that group better than the sniper rifle group imo.
that way, pistols becomes more of a sidearms/pdw group (ideal for concealibility/stealth) + has a broad range of weapons from tasers through to machine pistols (which is probably where the majority of shadowrunners/gangers are going to find their niche)
assault weapons are the guns you bring for a serious showdown, you're taking in an SMG for a high rate of fire over a short/medium range, an AR for greater range, and a shotgun for the real close up stuff. utility comes from shock locks, and full auto flechette suppression etc
precision/marksman group gets the battle rifles for marksman type roles, sniper rifles for the 3 mile kill, and hunting rifles for those who cant afford one of the other two types of gun :-)
as it is now, you can just take automatics. battle rifles for long range, AR'/SMG for medium, MP for close/concealable work. aside from taser/hand cannons you're not really missing out on much by just chucking your skill points into it, which is bad game design in my opinion.
as many of the other posters have said, the other groups should be equally useful within their role, there shouldn't necessarily be an "auto-include" that is good in every situation