So I've messed around with this before, but I thought I might take another stab at it. My goal here isn't to rewrite the matrix section or make it more realistic. It's just to make it more playable without taking it too far from the existing rules so that house rules don't spiral out of control as 5th edition builds on the existing content.
1) Signal Range (Addition to the game):
Every device has a signal range which represents it's ability to communicate with other devices without having to bounce the connection through the matrix. A device within signal range can be interacted with wirelessly without worrying about grid related penalties. Noise penalties between you and the target apply to your actions.
Most devices, such as commlinks, have a simple wireless antena that gives them a Signal Range of 10 meters. Specialized devices can have longer ranges. Radio Signal Scanners have a range of 20 meters. Cyberdecks and Rigger Control Consoles have a range of 100 meters, as do the living personas of technomancers. Note that to gain this benefit, the device has to be within your range, but not nessisarily the reverse. A Decker trying to hack a commlink can do so from 90 meters away and thus avoid any cross grid penalties, but the commlink owner would still take penalties from attempting to interact with the decker.
2) Locating Devices: (Clarification)
Any device within your signal range that is running publicly is automatically spotted and located to within about 1 meter. Devices in hidden mode, spotted or otherwise, never reveal their location without being tracked. The owner of a device can always locate that device at any distance as long as it's online.
Radio signal scanners are an acceptation to this rule. They automatically note the location, to within about 1 meter, or any device they locate.
Tracking an icon gives it's exact location to within a few centimeters.
3) Changes to PAN Slaving: (Rules Change)
Commlink or similar device can accept any number of slaved devices as long as they are within signal range of the master. Slaving continues to only provide defensive features, with no direct control over the device. Rigger Control Consoles have a limited number of special rigger control channels, equal to device rating x3, that they can use to link up devices, typically drones or vehicles, that allows those devices to be slaved at any distance via the matrix, and provides the autosoft/noise reduction sharing benefits to the devices in those slots as the existing RCC rules describe. Other devices slaved to an RCC behave normally.
Typically an entire shadowrun team will slave their devices to the cyberdeck of the decker for the duration of a run, so as to gain the benefit of it's sleaze and firewall, at least as long as they remain close to the decker.
4) Detecting The Presence of Hidden Icons: (Rules Change) - Edited with input.
To detect the presence of hidden icons within your signal range, make a special matrix perception test. The GM will compare your number of hits against the Sleaze rating of devices within range. Every device who's rating you tie or beat is detected but not spotted, giving you a count of devices but no details. Any device with a sleaze rating higher than your result must make a Logic + Sleaze roll vs your result to remain undetected. Masters in a PAN make a single roll for all the PAN. Devices you have already spotted to do not count in these totals.
Example: The security spider in a building makes a matrix perception test to check if any hidden icons are within 100 meters of his cyberdeck. He gets 6 hits, but the ratings of his deck limits him at 5. He automatically detects the number of any hidden devices with a sleaze rating of 5 or lower. Devices with sleaze higher than 5 must make a Logic + Sleaze roll to remain uncounted.
5) Marks, not Permission (Clarification)
There are two kinds of Marks: Legal and Illegal. Examining a mark does not reveal what kind of mark it is, but using an illegal mark typically requires a hacking skill roll while legal marks always work as they should. Marks hacked into place through Hack on the Fly or Brute Force are considered illegal marks and follow the typical rules in the SR5 Core book. Marks places through an invitation, including spoofed invitations, are considered legal and allow access to the functions of the device normally without requiring extra hacking rules. Thus a security rigger with 3 legal marks on security drone owned by the corp he works for can jump into the drone no problem, but a hacker/rigger with hacked marks on the drone would still need to make a hacking roll to jump into the drone.
If you have both legal marks and hacked marks on a device, you may make use of any actions on the device for which you have enough legal marks without needing to make a roll, but will need to make a roll for any actions requiring your illegal marks to be used.
If you are taking an action on a device for which you do not have enough legal marks, or no legal marks, but do have more than enough illegal marks, you gain a +1 dice pool bonus for each extra mark you have on the device. For example if you need 1 mark on a device to take a desired action on it, but you have 3 illegal marks, you gain a +2 dice pool bonus to take the 1 mark action.
6) Corporate Ownership (Clarification):
For rules purposes, Corporate Spiders are considered the owners of corp owned gear assigned to their watch. That means a corp spider assigned to a facility is not only the effective owner of the Host and devices slaved to the host, but also the devices in the building that are not slaved to the host, such as the guns and commlinks issued to the guards.
7) Spider Limits: (Rules Change)
Corporate spiders do not accrue Overwatch Scores for actions they take on their corp's turf. That means actions taken against icons owned by the corp, or those on the Corp's grid. Yes that's a serious bonus to AAA corps with their own national grids, but did you expect the Corporate Court to have it any other way? Of course Agents of G.O.D. never accrue Overwatch Scores, but they are suppose to remain somewhat neutral corporate conflicts.
This gets interesting when large corps wage open cyberwarfare on each other. GOD is intended to remain neutral, but in actual effect, they tend to take on a defensive role, with the agents of each corp's DemiGOD defending their own corporate grid while spiders, which are not restricted by corporate court laws, wage cyber-attacks. Of course shadow conflicts using disposable assets, runners, is open season to GOD agents across any grid boundaries.
8) Removing File Protection: (Clarification)
File Protection can be removed, legally, by anyone with the correct pass code. A pass code can be a few lines of text or numbers, a particular file, or even input from a biometric scanner. The particulars are set when the file is protected. A file must be unprotected in order to be interacted with at all.