I agree. Mass Effect should *not* have had Deus Ex's ending tacked on at the last minute. It should have had its own ending, one that didn't boil down to three choices paraphrased from another game. But the question wasn't "how would you rewrite Mass Effect to give it its own ending," it was "How would you have written things differently so that the ending we got fits?"
You may feel that it fits, but for many of us, most of us, it does not. The little themes and hints aren't enough. To properly present that ending, there should have been far more conversations about the nature of sapience, free will, the right to decide your own destiny vs. being directed by a power that 'knows better'. The player should have been thinking philosophically *back in the first game* and in the second game, long before reaching the finale of the trilogy. There's too many disconnects between what we experienced in the story (*especially* if peace was made between the quarians and geth) and the Catalyst's blind unquestioning faith in its operating parameters.
Well , actually, the Deus Ex form of the ending is because of the post-modernism aesthetic (which was the base of the writing of the trilogy from the beginning). But you can't say that because it superficially looks like Deus Ex, it's the same thing. It's not paraphrased from another game it's a referenced form, but it's actually totally different. That's post-modernism.
I know that a lot of people feel that it doesn't fit. The problem doesn't come from the game. The disconnection in the end was needed : the catalyst scene is a "high level" perception scene. Casey Hudson said it, and when everyone plays it the first time, it is surprising and yes, there's that feeling of disconnection. When you're in the event and when you take a step back to see the picture, you have to feel a disconnection. Mass Effect has an real important RPG aspect because the player who only experience the story, sees just like shepard 95% of the time. He is in the events and can't see the picture.
For the peace quarian geth it's the same thing : people can't see (or don't want to see) the context of the peace.
Well, on the fact that the player should have been thinking philosophically since the first game, I disagree because you can't do that in the event. Mass Effect work on different level of perception and the trilogy is based on that. The ending doesn't give the answers, only the clues to understand the trilogy.
And philosophical aspect isn't always when people talk and make explicit something. When some philosophers use a story in their book, they can use only the event and never quote any speeches (that's what they do most of the time).