You know, the thing is, well... if the whole thing is some great big simulation... how long has it been happening?
I mean, we assume that SR3 is real, right? Why? I mean, stop and think about it. We know Shaundi is meeting Shaundi. The SR2 one meeting the SR3 one. That could imply the SR3 one is a fake, right? Not that she was just caught in the simulation or something afterwards, but if so, why have a change? It's also in the same place we just spent SR3 in.. heck, even SR3 is a bit over the top. You freefall out of a plane for over 15 minutes, get to take down a number of gangs to rebuild your empire (much like SR2), have to fight the national guard and even a goverment super-science backed army. You even have zombies at one point!
Honestly, a simpler solution is the whole thing from the start of SR3 on is part of the simulation. It was all a big dream, and that's going to be how they start you off at the ground floor: You never actually DID any of the big stuff of SR3. SR2 happened, you took over Stillwater and Ultor.. then at some point were captured by aliens (or maybe that was all simulation too, not sure how far we're gonna have it go back, but the presence of 'old' Shaundi implies a difference). Gat never died, because that whole part never happened.
Of course, the alternative is as said this is just part, with people reliving Gat's death in different ways, and the whole two-Shaundis thing is her confronting her old self and how she's changed. We'll see.