I already addressed this in previous posts in this topic, but here goes,
If the 3rd part of a story dumps *everything* its predecessor put forward, of course the 2nd part is going to look detached and stupid. Instead of making what they had already done work somehow, it was flushed down the toilet without any attempt to save face. Saying ME2 was already wandering down a different path maybe true enough but what's the point in spiriting away to an entirely new thread? What could have been done in ME3 is entirely academic anyway. All I am saying is that it could have continued from what was established in ME2.
ME3 didn't dump everything ME2 put forward. That's rather the problem, because ME2 didn't put a plan forward in the first place- and much of the stuff ME3 did drop was largely unworkable or unthought.
Dark Energy remained as technobabble it always was. The squadmates were reflected for being dead or not. There was still no clue as to WTF the Reapers were actually trying to do. ME3 still built on ME2's end-game (and DLC's) implications that victory wasn't going to be by the Cycle's own strength, but rather from some macguffin from the past.
ME3 could have chosen different elements from ME2 to build on, but they would have all been equally arbitrary implementations and made-up-on-the-fly. ME2 was always going to be detached because, again, ME2 never planned how anything would attach to it.
As for the fate of the squad mates suddenly being important to their arcs in the 3rd game, consider this,
1. Shepard can *also* die. Yet we have a 3rd game featuring him as the main protagonist. There's no Lazarus Project 2.0 in ME3 to hand wave that away.
There's also no import if Shepard died. It's explicitly a non-canon outcome of the Suicide Mission, just like dying with Morinth.
2. The fate of the Collector Base makes no difference either way in the 3rd. The ME3 plot doesn't reference it meaningfully at all. It doesn't expand upon the 'techno-babble' of the 2nd, it is just ignored and only serves as a checksum for having additional choices depending upon EMS (whatever this was supposed to mean anyway). It may certainly have been stupid to impose that choice but it's evident now that nothing was learned when the rainbow ending was imposed upon the end of ME3 again.
The fate of the collector Base doesn't matter because 'destruction' is the same concept as 'death' with characters: all plotlines have to accept the absence when being created. Short of entirely differing plot narratives- which Bioware has repeatedly declined to do because of resource restrictions- or letting players get epically screwed over by a choice of the previous game- which would be antithetical to Bioware's general proclaimed design philosophy with ME's moral choices- plots will run by the lowest common denominator. Whatever can be justified by the 'destruction' route, in other words.
This extremely foreseeable problem, just like the rest of the suicide mission's casualty implications, was seen back after ME2.
If ME2's writing had a plan for what the Collector Base was supposed to do, it might have helped- but it's rather apparent they didn't. They just punted, when they never should have.
To me it's quite clear 'choices' and 'consequences' are not something that was understood during the creation and production of this series. The interpretation of these two words is all over the place. Because if the 'consequence' of Shepard dying in ME2 is meaningless, why does it not apply to selected squad mates from that game as well?
Because Shepard dying was something the devs said even at ME2's release was non canon. It is impossible to import a 'Shepard dead' Suicide Mission into ME3. ME3 only begins with an import save of Shepard surviving, or no save with shepard surviving.
But you are correct that consequences were never thought through. That was never more apparent than in ME2, which dumped the previous game's end-game decision (and ending) to go it's own way by dumping the -insert final council- here and the acceptance of fighting the Reapers, didn't even provide cameo/reflection content for a number of possible ME1 choices (which themselves, for all the core plot choices, were variants of 'kill X or not'), and didn't even concern itself with deciding what the Reapers actually want to do even as it made revelations about the Reapers the big plot reveal.
Fortunately, bringing us back to the subject of the thread, these were all things ME2, not ME3, is responsible for.
It's similar to passionate discussions people used to have on this place 3-4 years ago ... discussing which ME3 ending would be canon and such (not that I want to revive that again ... god, no).
Except there's an actual answer to the ME2 suicide mission, hence why there was no passionate debate about Shepard's survival 6 years ago in ME2. It wasn't in question.
Shepard survives the suicide mission. Anyone else can die. That's what's canon compatible.