This post is one giant spoiler so if you do not wish to be spoiled, do not highlight the white text to read it. After doing two play throughs of the game, I have come across several problems with how the story progressed. Im not even touching the endings yet.
My consensus is that this is a deal with the devil. We get our ending... we get what we want, but in the worst way possible. Its like the star wars prequals. They all sucked, but you had to watch them. There was no getting around it. You HAD to watch them.
First problem. Humanity is the second target, yet the primary focus of the reaper invasion. Sure reapers are sent to other planets as well, but their main focus is earth. More reapers are there than any other planet. Why is this, when we know that the turians have the most advanced military in the galaxy and the best land forces outside of the krogan.
It could be speculated that the events of mass effect 2 made harbinger sort of mad at Shepard. So we took the largest force to earth. However this would conflict with the events of the ending.
(Spoiler alert.)
If you remember, the catalyst said he controlled the reapers and that they were his solution to the problem of synthetics like the geth who would eventually become so powerful that they would kill anything that had DNA.
The next problem ties in with the first. Why in the hell would the reapers focus on earth instead of attacking the citadel and shutting down all of the relays. That was their original plan wasnt it? Remember in Mass effect one how the plan for the reapers was the shut down the relays and cutting everyone off to be harvested? (Sorry spoiler alerts are null and void for both me1 and 2. The games are old now and you should have played them already since they are both amazing and fun.)
Instead, we have the point of something I like to refer to as plot convenience. And as red letter media happily put it. "Plot convenience = movie suck." While this isnt a movie... it works nonetheless. But never fear people this is retconed.
(Spoiler alert.)
The reapers actually go and take over the citadel as they figure out that humanity learned that the catalyst is actually the citadel. But this does not shut down the mass relays as the prothean AI on Ilos said it would in ME1. It simply gets moved and turned into a giant harvesting chamber that is used to make reapers... WHAT!?
While several things were done right in the game, especially the political bickering between certain races and the actions you must take to apease these faction. It all goes horribly wrong.
For instance. Why is the focal point of this game about taking back earth? Why not Palaven or thessia, or mars or whatever. Why is it about earth? I know thats where we live, and it makes for an epic story, but this is an expanded universe the size of star wars and star trek. There are dozens of races, hundreds of worlds, and trillions of lives at stake. But I guess that would be the point of the plot convenience. Since it was convenient to make earth the primary focus of the invasion, you make earth the primary focus of the counter attack. That way you kill off the largest focus of reapers, you have already won.
It seems like bioware really dropped the ball here, or EA forced them to push the game out. Im going with the latter as Bioware wanted the game delayed ever since the russians hacked the demo and leaked the entire script forcing bioware to change it. Which brings me to the final part of this ME3 hate
The endings. From here on out it is spoiler. Dont read if you dont want to know yet. You have been warned.
((((((Spoiler alert. Im telling you all 6 endings here. Yes there are 6.))))))
No matter what you do in the game, no matter which decisions are taken, no matter who you side with, it doesnt matter one tiny bit. You get 2 default endings. If the green bar is filled completely, no matter what your galactic readiness is at, the energy wave does not wipe out life on earth. If it is not, it does.
But there are three choices too. You have Control, destruction, and synthesis.
You can choose to destroy all synthetic life. This will kill the reapers, the geth, and most of the technology you rely on. This sends out a red shock wave that either washes over harmlessly, or kills all life on earth depending on your effective combat meter. The citadel blows up, killing shepard and anderson, and destroying all mass relays. There is no stopping the death of shepard. Or the relay destruction. It will happen. No matter what.
You can choose to control the reapers. This will kill shepard, yet preserve his/her spirit and shepard becomes the new catalyst I suppose. Shepard calls back all reaper troops and you see soldiers on earth cheering, or dieing in a fire depending on that green meter. The relays are destroyed.
You can choose synthesis which merges biological and synthetic life into one matrix. Once again, depending on our meter, the wave will wash over or destroy earth. The relays are destroyed no matter what.
In all three endings, you see the normandy flying at FTL speeds trying to escape the shock wave. But the wave engulfs the normandy and its inhabitants are marooned on a strange plant. If your bar wasnt filled, you dont know what happened to the crew. You see the door crack and then the credits roll. If you filled the bar, some of your squadmates and joker walk out. If you get the good ending, after the credits, you will see a man and his son talking about shepard. With the boy asking him to tell another story of the shepherd. The father says OK and the screen fades to black leaving interpretation for another mass effect.
So there you have it. No matter what you do, no matter who your friends are, no matter who you saved, no matter who you kissed undressed saw their boobies and the rest, it doesnt matter. You maroon every race's navy in earth's solar system and shepard dies. There is no storybook ending here, and I am strangely fine with that, but I just feel like the entire game was nothing more than a tease. Like you actually had a say in what happens. NO You only decide what color the explosion is in the ending. THATS IT.
You could argue that controlling the reapers would allow shepard to build new mass relays, but that could take months. I highly doubt earth's shattered ecosystem, and the quarian liveships could feed all those people for that long of a time.
So my consensus. EA sucks for pushing the game out too fast, and those russian hackers REALLY suck for forcing us to eat this stinking turd of an ending. 
