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The big split is more AR vs VR. To do anything in previous editions, the decker should be exclusively in VR and thus dead to the world. However with 4th's advent of AR, the hacker can now be more than a dead body and still function well in the matrix. This is the factor, more than anything else, that encourages the hackers to go along with the team- because it's interesting. If the hacker is off in VR (doesn't matter where, in his bed or in the facility), his presence is not with the rest of the team. This splits the GM's attention, and if the hacker's time in the spotlight takes a long time while he's also in VR, this will inevitably lead to "pizza time" no matter what rule set or setting you use.
AR on the other hand, allows the GM to avoid "splitting the party" and the hacker is allowed to be in, more-or-less, the same narrativistic scene as the rest for the runners, which hopefully eliminates "pizza time" and that is the encouragement to infiltrate with the rest of the group. If you're looking for in game reasons to support that... I'm not sure you're going to find a super compelling argument either way, but it won't be the first, last, or even close to the worst aspects of the setting that breaks under the scrutiny of "realism."
This wasn't quite the case, since you could shut off the RAS override in earlier editions, and going full VR conveys serious benefits in SR4.5. Even though I've done my best to get the decker to go in physically with the team, they always drop and go full VR when there's serious decking to be done. Unless I deliberately fail to tell the player all of his options, they will choose to use full VR if they have a lot of matrix work to do, and only use AR for less serious things or when they don't have much time to switch.
My biggest "pizza problem", however, is Legwork. Frequently, the team will come up with a list of questions for zillions of things, hand it to the decker, then leave for food while he rolls a crapton of Data Search tests. Most of those leads will never pan out, or will go toward plans that will never see the light of day. I do my best to make sure the leads that do pan out require in-person interaction to fully chase down, but the decker pretty much dominates the legwork section. Since most of these searches pretty much amount to advanced Googling, I can't fairly demand that the team chase down all of these in person.
For example: tonight, I sent the team to infiltrate a DocWagon facility. They asked a bundle of questions before they even formulated a plan. Some I had anticipated, some I had not. The key thing here is that it was important enough to require a roll, but not enough that I needed to take it to a face to face meet or other fix. For example, getting the shift schedule is something the decker should be able to do purely on the matrix, as is floorplans, names of key personnel, and so on. Like any smart team, they asked a lot of questions; and since many of them were dead ends, there's no point in doing anything more than a web search for most of it. Based on that data, they formulated their plan.
The problem was, before they could make a plan or decide which leads to chase down, the decker spent an hour doing Google searches. That's pretty damn time consuming. The decker pretty much dominates the legwork, and who can blame them? By having the decker eliminate a lot of the dead ends, they can focus their questions to contacts and others to the important issues, instead of wasting time. Unfortunately, this leads directly to the Pizza Problem.