SimonG: Obviously you couldn't do this in the proper ending, as that would have exploded the production costs. But over the course of the game, you got E-Mails, dialogues and galaxy at war scores that reflected every decision you made in the game.
Personally I always considered that a very easy and cheap way to handle choices and consequences. You just need some summer job writers to spend 10 minutes writing an e-mail and have some devs spend 5 minutes adding an IF in the code and voila you have a new "consequence".
You could easily create a DN3D mod that do the same and make that, for each alien you avoid killing, you receive an e-mail form his family thanking you for letting him live; if would be easy to do but it wouldn't make DN3D a games loaded with meaningful choices and consequences.
For the military readiness, it's closer basic achievements than anything else, no matter what choices you made you can easily boost the value my playing 1 or 2 hours online and have access to all the endings.
IMO ME is a very mixed bag when it comes to handling choices and consequences, it does some great/good thing with it, the way the relationship between team members were handled for example, how having a "romance" didn't just mean some lame PEGI-3 love scene but had impact on several conversations; that was handled very well in ME3 (Much better than in DAO or other Bioware games).
But on the other side there was plenty of big "universe shattering" choices that in the end had very very little impact on the actual game itself; if you were lucky you had at best one or two dialogs change and a bunch of e-mail. Kill character "A" then character "
not A but a close enough copy" will take its place and give you the same missions and let's not mention choices that were "reseted" to their default state because the Devs didn't knew how to handle them.
Personally I consider that Witcher 2 did a much better job with choices and consequence, there was of course a lot less choices and most (i.e. 99%) of W1 choices didn't carry over, but there was more choices that had a "real" impact on the game, totally locking some parts of the story while unlocking others.
Of course I am realistic and I never expected to have thousands of branching paths for all your little choices, but having at least one or two for some of your major choices would have been nice; not just some silly e-mails, some spreadsheet scores, or at best some different cut scenes.