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I've seen a lot of people having problems with this. Let me give you my advice. I do this almost every time and no one dies.
First: Make sure EVERYONE is loyal. It's possible for some squad members to survive without loyalty, but having them all loyal makes it a hell of a lot easier.
Second: Ship upgrades. The only upgrades that make a difference are:
'Thanix Cannons' (the weapons) You need to talk to Garrus for this.
'Cyclonic Barrier Technology (CBT)'(The shields) Talk to tali for this.
'Silaris Armour' (The armour') Talk to Jacob about this.
You only need these three upgrades for you crew to survive the three 'ship deaths'.
Third: Specialists. (Loyalty is required for the participants to survive)
1: The vents.
Tech expert: Tali/Legion/Kasumi (I use Tali)
2nd squad leader: Miranda/Garrus (I use Miranda)
2: Sending someone back with the crew. (Optional and you won't be able to use them for the rest of the mission.)
Escort: Apparently anyone will do. (I use Mordin. He is weak and may die later on. I will explain more about that in a bit.)
3:Seeker swarms.
Biotic specialist: Samara/Morinth/Jack (I usually pick Samara/Morinth)
Second squad leader: Miranda/Garrus (Again, I use Miranda)
4: 'Hold the line' Final stage.
Everyone except the people in your 3 man squad will stay behind to hold the door.
Here's the annoying part. There are apparently hidden survival 'points' for each squad member. I'm not sure what they are exactly, but if you get a bad number then some of the people holding the door may die. I played around with the squad selection a bit and the theory seemed to be true.
The best way to get around this is to take the 'weaker' people (with the worst points) with Shepard. They are: Kasumi, Mordin, Tali, Jack and Miranda.
These people will often die if left. If you take two of them with you and they are loyal, they survive the fall after the final boss as long as they are loyal. The remaining 'weak' people will have their points negated by the 'stronger' people left behind and should survive.
This is what I do. And it works every time. Let me know if it works. I don't think I missed anything out... If I have just say.