Mass-effect – What am I missing having lost the Normandy’s crew at the end of ME2

The following is the memorial plaque wall when you start with a new character and select the "numerous" option. As you'll note, most of the squad members from Mass Effect 2 are still alive:

Those names underlined in blue are the original crew members of the Normandy SR-1 who died in the beginning of Mass Effect 2, along with the two squad members Ashley Williams and Urdnot Wrex (marked by blue squares). Kaidan was chosen to be alive because I was playing a female Shepard; when playing a male Shepard, Ashley will be the Vermire survivour.

Those names underlined in orange are all crew and squad members from the Normandy SR-2. Those marked with an orange circle, Gabriella Daniels, Kenneth Donnelly, and Kelly Chambers, would have all made notable appearances in Mass Effect 3 had they not died. More specifically, the former two can be brought back aboard the Normandy in their usual positions as engineers, and Kelly Chambers is a potential romance/fish keeper* depending on your interactions with her in the previous game.

Thane Krios and Jacqueline Nought (Jack) appear to be the only squad member from Mass Effect 2 that's listed as having died, and are highlighted on the wall by the orange square.

Everyone else not on this list is presumed to be alive, and not one of the "numerous who died." In particular, Garrus, Tali, Miranda, and Jacob are all listed as alive. However, the game will act as though you never met Samara/Mordinth, Grunt, Katsumi, and Zaeed, effectively killing them. It will also act as though the original Council died during the attack on the Citadel in Mass Effect 1.

^{*that is, she returns your fish from Mass Effect 2 to you; you need the aquarium VI or extreme patience to keep them alive}

The problem of course is that this is the same list of people who would have died if you had simply chosen the Ashley/Kaidan option. In comparing the two save files, one from a "numerous" selection, and one from a "Kaidan" selection (using male Shepard to keep a consistent Vermire casualty), there's actually very few differences between the two scenarios.

The tables below illustrate the difference in game variables before you perform any action:

PlotID  | Numerous | Kaidan dies
--------+----------+------------
17807   | true     | false
18005   | false    | true
18122   | false    | true
21569   | false    | true

PlotInt | Numerous | Kaidan dies
--------+----------+------------
10393   | (unset)  | 3

At the moment it's unfortunately unclear what these changes represent, because they don't directly map to any of the significant and/or labeled plot events that the game has. Presumably they have some noticeable impact, however, so I'm going to keep digging until I get to the bottom of this.

Lots of spoilers here, so be warned.

Here's where you find everybody

• Thane will die regardless due to his advanced Kepral's Syndrome. However there is a way you can avoid Thane's death but know that another character will die in his place (Video). You can view the details in the question, Can I change what happens to Thane?.

• Mordin will die curing the genophage. I've heard that the only way around this is to not have Wrex survive Virmire, and also have the female Krogan die.

• Miranda can die. Here's how to avoid it.

• Legion will die. Either he's killed or he sacrifices himself. Tali can die in the same mission if you side with the Geth. You'll need to save the pacifist Quarian admiral, and have a high paragon to save her. I've also heard that you might have to have imported a loyal Tali from ME2 as well.

• Samara can die as well. A high paragon and an interrupt saves her.

• Grunt will die when you meet up with him if you try to save the Rachni Queen and he was not loyal from ME2.

• Kaiden/Ashley can die when trying to save the council from Cerberus. Again, high paragon and an interrupt save him/her.