Mass Effect 3 pissed me off to no end. The game is good, but the entire game they emphasized the choices you make and even use save data from previous game choices to impact the game, then you get basically the same ending regardless of your choices. What was the point of all that if it turns out the same anyways? *Shakes fist at BioWare!*
That's been pretty much the case throughout the entire Mass Effect series though... the vast majority of the choices and consequences are largely cosmetic and put you in the same position regardless of what choice you make.
Kill or talk down Wrex in the first game? Another character comes in to basically fulfill the same role in two and three.
Free or exterminate the Rachni in the first game? No real change to the plot when they reappear in the third (basically you get some different dialogue and a new number on your warscore).
Destroy or save the Collector Base in the second game? No real difference.
How the Citadel Council is made up at the end of Mass Effect 1? Changes a few lines of dialogue.
Choose Udina or Anderson at the end of Mass Effect 1? A few dialogue changes.
Cheat on your Mass Effect 1 romance in 2 or your 2 romance in 3? Few lines of dialogue.
I could go on...
The only choices that really make any difference are which squad-mates live or die... but even they're somewhat minimised. Sure, Kaiden or Ashley die in the first game... but the only plot changes are extremely minor and in gameplay terms you have other squadmates who can do basically the same role (as is the case if Tali or Garrus die in Mass Effect 2). Likewise place-holder characters are inserted for other squad members who die during Mass Effect 2 for Mass Effect 3.
Bioware's approach to C&C has pretty much always been cosmetic. You get a different line of dialogue, you might get a slightly different cut scene, a new character may appear to fulfill the same role and in Mass Effect 3 you might get slightly more or slightly less points towards your War Score... but that's it. It's about the illusion of choice as opposed to real choice. I can't say I particularly blame them... Bioware's strength has rarely been in detail C&C and considering how if looked at in any great detail the entire Mass Effect plot (both of the series as a whole and of the individual games) collapses into a mess of plot holes and things that don't make sense adding more significant consequences to your choices would have likely created even more issues. Bioware played to their strengths which is "epic" storytelling/moments and a large cast of NPC's.