You have to admit the ending is pretty damn horrible. The little boy that created the reapers to wipe out organic life in order to save life from being wiped out by synthetics is laughably idiotic. Who the hell wrote that? And the whole 'organics and synthetics can never get along' is shown to be false earlier in the game when you make peace with the Geth. Frankly there should have been a choice to tell that little god child to 'f' off and take his circular arguments and Reapers with him and never come back. Bioware succeeded in ruining their own franchise in the last 5 minutes of it.
Next we'll have Bioware.. or rather EA releasing DLC that explains all the plot holes, fixes all the crap endings, adds a new one or what ever. But of course, it won't be free.
For those who don't understand why everyone is up in arms over this, here's a good video explaining it all.