^That's debatable. I mean at least it was something new to fight and actually expanded our understanding of the reapers a little (whether that was something worth knowing is neither here nor there.) The ME1 end boss was just a reskinned geth hopper chucked into an enclosed space.
The problem with the human reaper was that it changed the overall tone of Mass Effect into a more condensed and quite honestly, contrived storyline that slowly got worse. It essentially all boiled down to "Humans are special" and that we are the Reapers #1 threat and target. I hate it when we have an entire universe full of diverse aliens with their own unique strengths and weaknesses that the franchise all of a sudden resorts to having humans be the cream of the crop. This is why I like the first Mass Effect game over 2 and 3 because it didn't portray humanity like that. Humanity wasn't the center of the galaxy, they were, like everyone else, just a part of it. Shepard isn't awesome because (S)he's human. (S)he's just the hero who happens to be human. I don't see why an Asari, Turian or even a Krogan couldn't accomplish what Shepard set out to do.
It's like Gene Roddenberry took over writing duties for the series after the first game and brought his "If we aren't telling a story about humans, what's the point in telling a story?" ego with him.