I have no problem with Shepard dying to end the series. As I've said that would be a fitting end taking out the reapers. I guess the thing the confuses me the most is the Catalyst trying to keep synthetics and organics from attacking each other, by attacking organics with the mostly synthetic reapers.
ALSO, the endings in ME2 and ME1 weren't exactly the same. The end of the game conversations had drastically different dialogue depending on your choices at the end of the game. In ME3 the exact exact same cutscene happens to the end the game.