To all the people asking "Why would they disappear?", they pretty much have to, or perhaps simply make a few cameos. Why? Simple!
Each and every team member could die. All of them. You could be the sole survivor. That means that Bioware has to plan the next game around that scenario, as well as the one where everyone lives. Now, considering that by this time people expect all party members have questlines and such and interact with each other, the sheer number of combinations that have to be taken into consideration would be a logistical nightmare. So, it's either cardboard cutout squad, or most of them go away.
Now, I'm guessing we'll get to keep a few of the gang. We got to keep Garrus and Tali, I'm expecting that a few will stick around in your squad in ME3. The rest may or may not appear as NPCs, kinda like Wrex did.
As for the question of "How you all got split up?", my money is that Shepard was visiting Earth when the Reapers hit and his squad simply can't get to him...