I haven't played SR3 so my answer will be entirely based on my experiences with SR5.
Deckers don't seem too separated from what's going on in meatspace
The Matrix in SR5 is completely wireless (although I believe this may not have been the case in earlier editions) and functions more as an alternate plane of existence than as a completely separated network of computers.
The Matrix can be viewed (using the appropriate devices) either as Augmented Reality, which is overlaid on their natural vision or by entering Virtual Reality and leaving their meat body limp and unconscious. The VR Matrix closely models the physical world, with connected devices and people appearing as icons and personas respectively.
While operating in AR a Decker uses their physical Initiative to determine when (and how many times) they get to act. Since this is unlikely to be as high as a Street Samurai or similar quick combatant it means that while the Decker can still operate, they're limited in how much they can comparatively achieve but make up for it with the ability to keep moving along with the rest of the team.
While operating in VR a Decker's body is completely limp but they can still observe their teammates (via their personas and/or devices) and communicate with them. They can no longer move their body around or take part in physical combat but use their Matrix Initiative instead of their physical Initiative, allowing them to act faster and more times each round. Regardless, their actions are still 'in sync' with what's going on in meatspace and isn't a separated thing.
Other benefits of the Wireless Matrix
Deckers aren't just limited to breaking into data vaults or disabling security systems in SR5, anything with a wireless connection to the Matrix is a potential target, this can include various fun-to-hack things such as Smartguns, Cyberware, Drones and Vehicles. Your Decker may be crouched behind a desk, their body limp as they hack away in VR but they could still brick a security guard's smartgun at a critical moment and save the Mage from taking a bullet without interrupting whatever else it was they were doing.