So far they come on B-wings, E-wings, Shuttles, and TIE/Phantoms. It seems to me FFG is using the systems upgrade slot as a way of denoting 'advanced/next-gen ships' and not actual specialty systems. For example, the A-wing is the first ship described as having a 'system' and used it to jam radar and communications. Yet it doesn't have one and is largely considered "soft." But the B-wing does and is already fairly robust. So what exactly are systems upgrades meant to represent? Just next-gen ships? All the other upgrade slots are taken directly from the ship lore and this seems the first one FFG has kind of invented but I'm not sure I can see what makes a ship/card eligible for the systems title.

(Yes, the upcoming Decimator has a modification card called "Tactical Jammer" which, if it's not Imperial or large ship only, could be used on the A-wing. But that's both hypothetical and a single option.)

Fluff wise...

I'd say they represent a ship that has a few optional systems that may or may not be installed. Take the older ships like the X-Wing, Y-Wing, Z-95 and many of the Ties. They were for one reason or another produced in such a way that they didn't have many options... In the car sense.

B-Wings, E-Wings, Shuttles however most likely had systems that could be installed or removed depending on the mission requirements.

There is no real canon for this, so I'm going to guess that FFG limits it to advanced ships or larger ships that make sense to them at least. It's also undoubtedly part of the mechanical balance system for each ship. It's also a way to further separate ships... A B-Wing without the System Upgrade slot would be a lot more like the X-Wing then it is with it.

With the (fairly) new 'modifications' you can customise your ships.

Some ships however are more equal than others and are allowed to have more options to customise.

They are computers basically.

I know that sounds like a cop-out in lieu of a answer with more "meat", but I think it's as close to true as you can get.

Black boxes, pods, and other things. Way back when , when I was in the Army, I worked on aircraft survivability equipment. IR and radar Jammers, threat receivers, flare and chaff dispensers, etc. Non of which were needed for flight, but would be very helpful when the crap hits the fan. Thats what I guess these things are.

I'd also go with computers. They represent advanced systems that aid pilots in avoiding obstacles or ships (Advanced Sensors and Enhanced Scopes), evade fire from distracted enemies (Sensor Jammer) or maintain targeting solutions on a designated hostile (Fire-Control System).

These all make sense as to what they are, it just seems like A-wings, TIE Defenders, and maybe even TIE Bombers would get them. Heck, all the freighters too. Though I'm more willing to let the slide in an odd way because they'd be OP.

Don't get to lost down the rabbit hole of what real analogs of Star Wars would be like, first it is a fantasy setting with only passing resemblance with actual reality and the accompanying physics, second it is a game balance tool, so the use has to be limited artificially for balance.

(Yes, the upcoming Decimator has a modification card called "Tactical Jammer" which, if it's not Imperial or large ship only, could be used on the A-wing. But that's both hypothetical and a single option.)

You've also got to remember that a few Rebel ships can carry an astromech, and with the range of astromechs now available, that also gives a fair amount of flexibility to some of the older ships in lieu of a systems slot.

I don't know, but I really liked the Sensor Jammer, greettings.

A card that "jammed" abilities or pilot-to-pilot buffs (like preventing communication) would be cool.