So, if Turians and Quarians have approximately human lifespans, then buy moving the universe forward, say... 400 years, you're realistically only going to have Grunt and Liara kicking around from Shepards team. We know Wrex is already an old Krogan, so going forward that much, he should be gone (not to mention I imagine Krogan clan leaders" have about the same life expectancies as Klingon chancellors, so it's safe to say he won't be around for too damn long...). Team that with Liara's new job from the DLC... I won't spoil it for the two people who haven't played it yet... she probably won't be playable in future sequels, but obviously could have an effect on the universe. That basically leaves Grunt, and I'm OK with that. I would say Legion, but since even he admits he is not an individual... I'm just going to let that drop.
As far as incorporating the data from ME3... as others have said, I imagine that all roads in ME3 lead to the Reapers being defeated. I'm guessing it will just be in the details as to HOW that happens, which could lead to some slight differences in how the universe starts off in an ME4... but ultimately they could just write whatever they want so things more or less start the way they want it to. For example, we all know SOMETHING is going to happen between the Geth and the Quarians in ME3. Say Shepard convinces them to work together, and in the "happy" ending the Quarians get their world back. Now, if ME4's plot requires that the Geth still hold the world, then all they have to do is say something like Quarians died in large numbers, their immune systems just could not re-adjust, and so they willingly chose to go back to the flotilla, or just died off, or whatever they want to say. I think that they are going to want to start relatively fresh in ME4, so that the only changes are going to come in backstory, maybe a few different characters in different places, etc. not multiple drastically different starting galaxies.
All that said, I wouldn't mind if they did a prequel side game or two before jumping into a new epic ME4. A Gears of War-esqe shooter set in the Turian War would make a fun little diversion. I also think I would enjoy a RTS set during the Rachni War. Since we know the Krogan and the Rachni both have (well, had...) very high reproduction rates, i think that could very well lend itself to that genre. Just my silly thoughts.