The only problem with the ending is what happens after you make your choice. The choice itself is fine. The endings being differentiated largely by what color of light fills the screen is a cop-out, and the final cutscene should have shown some drastic changes based on which choice you made, showing a few consequences for the people who lived in your game and other long-term consequences for choices made throughout the trilogy. Death of the main character, destruction of the Mass Relay network, the workings of the Crucible, these things are perfectly fine. The only issue with the ending is that it doesn't show various permutations, so it doesn't feel like player choice made a powerful consequence. The ending should have done a Fallout-style checkup on various civilizations and other people.
All the same, everything about the ending itself up to the actual choice makes sense and is actually really good and solid. The ending cutscene itself is problematic in that you choose a color of light and affect a couple other very small cosmetic changes, even with the "middle road" option which should look far more drastically different than it does, but the idea behind the ending is something I wholly support. I wonder how many people are stumbling around saying "THE ENDING SUCKS IT'S SO OBVIOUS" and agreeing with each other when their reasoning itself is drastically different from that of the next fellow over.