I suppose I, like many others, probably misunderstood the original brief, thinking that "Stop the Reapers", was synonymous with "Destroy the Reapers", much as "Stop the Blight" was synonymous with "Kill the Archdemon". Have to admit that when you change the viewpoint, then having a Destroy or Control ending it perfectly reasonable but Synthesis just didn't make sense, particularly when you saw the result. It required suspension of belief just a step too far.
Having Reapers still very much present in two of the endings and yet gone in the third, whilst the rest of organic life is unchanged in two endings but totally altered in the third, is a bit problematic when it comes to stories set post ME3. Since we so enjoy playing in the Mass Effect Universe, it is natural that we would like to continue to do so and this is what upsets people, that you can't see how this can go forward based on 3 such diverse endings.
I also disliked the colour coding of the choices. Having conditioned the player to regard certain colours associated with certain actions, it made it appear that the colour of the choice determined its validity to the way you had been playing the Shepard character. It would have been better for there to be no colours but simply right, left or centre.