There are several aspects of the ending of ME3 that bug me. They start with the mission to Thessia. Kai Leng shows up (we’ll ignore how horrible his character is here, that’s a separate issue) and you have to fight him. Fine. So you fight him, and you have to “win” the fight, ie. not actually defeat him but get him below x% health. And then there’s a cutscene where you’re defeated by a gunship. What? I mean, I get that the plot dictates that Kai Leng has to make succeed in getting away with the Prothean VI, and that’s fine. But if the plot dictates you must be defeated, then have the player defeated. Like in the Arrival DLC. I hate in any game where you succeed in a mission and then get beaten in the ensuing cutscene because of the dictates of the plot. This is a particularly egregious case.
Next, the offscreen “oh BTW the Citadel has been captured” renders whole swathes of minor quests and conversation interventions in the game ultimately futile. The various people you helped, the shopkeepers, the refugees down on the dock, the medical clinic. All gone with a snap of a finger.
Finally, some gaping plot holes at the end. The Normandy swoops in to evac your squadmates. What? If it could just show up there, then it ought to be disgorging every last crewmember that can hold a rifle to sprint towards the conduit, not just saving Liara or Garrus. Is the fate of the galaxy on the line here or not? Then we pass through the conduit, which the Reaper forces clearly know about because they’ve been defending it, and we’re met on the other side by…nothing. Are the Reapers super-intelligent and overpowering, or aren’t they? They can snap their fingers and take the Citadel without a fight, transport it halfway across the galaxy, but they are powerless against one soldier almost dead on her feet limping through an empty corridor? They know you’ve been transported there, because they’ve just been defending against you getting through!
The glowy kid and the magic ending choices actually don’t bother me so much. Well, I don’t much like that the synthesis ending exists, but that’s not a problem because I can just not choose it. It’s the sections before where they snatch agency away from the player by having the setbacks occur in cutscenes/off screen, and the nonsensical bits near the end that grate on me.
That said, I think the biggest problem with ME3 is just that the writers had painted themselves into a corner. A single reaper is nearly enough to defeat a massive combined fleet in ME1, and now there are thousands of the things, plus their minions. Hence, the Crucible. Okay, but at every turn the Reapers should be able to just wipe you from the map. Given the level of mismatches we see in the cutscenes showing, for example, the Turian fleet vs numerous Reapers, the entire war should be over in a couple days. In many ways the entire game doesn’t make any sense because the are constantly switching from overwhelmingly powerful to surprisingly easy to defeat depending on the needs of the plot. And it’s difficult to see how this can be fixed without modifying huge chunks of story that was already fixed in place by ME1&2.
And so, we just enjoy it for the awesome characters, and pretend not to notice the incoherent parts.