We used the matrix quite a lot compared to a lot of replies I see here. This was back in 4th edition, when the hacker was just walking along with the rest of the group.
In combat I've never seen the problem. The hacker just rolls his matrix initiative, just as the rest rolls meat initiative (or astral if that comes into play) and you just add the hacker in between everyone else. No matter it's a completely different world, he just goes whenever the initiative tells him to and then it's the next person/thing/spirit/whatever, and he gets initiative passes just like everyone else, depending on what he's doing and what gear he has.
Outside combat we've never had much trouble with it in our group either. Maybe because the GM was a matrix fan and knew the rules quite well, as did the player. And indeed, sometimes it takes a while to resolve something, but if the face is trying to talk to someone, it can also take a while. That's the GMs job to jump between the two (or more) groups.
And yes, sometimes the GM stays with the hacker a bit longer when other players use the opportunity to take a toilet break and that's fine too. In fact, I sometimes hold a bit and go to the toilet when the GM is in the zone with another player, so they can continue their thing without having to skip back to me. In fact, I've seen the GM do the same, while we were doing some planning (and you know how long that can take in Shadowrun): 'you just keep thinking and planning this, I'm off for a bathroom break'.