If they didn't explained how it works it's because they wanted to create that kind of ending : make people think that it is a super weapon when it's not.
In the destroy ending it pretty much does what I would have expected from a super weapon.
You have to consider that the super weapon ending is easy to write and please the majority of the players. That's the easiest option to end, that's the "lazy writing".
Yes, that's even lazier, although, paradoxically, it might have provoked less protest. But I think it is quite possible to avoid some of the problems of the ending, without making many changes to the game and the overall story. Let me try (I'm not a writer):
This is before Shepard collapes at the control panel: The crucible does not fire because Harbinger has taken control of the catalyst (no need to explain exactly what that is, but can be added of course). A projection of Harbinger (like Sovereign in ME1) appears and explains: The reapers are programmed to protect life in the galaxy from anihilation by technologically but unstable advanced civilizations. Every civilization evolves from beings that have to fight for basic survival, so each has the roots of aggression in it. The reapers are waiting for a civilization that is capable to control these roots while advancing to a stage where it could wipe out all life and all life-supporting planets in the galaxy for ever, yet in the previous cycles the risk was deemed too great. In this cycle, the rise of humanity with its great potential has prompted the reapers to act. The reapers have waited longer and longer in each cycle in order to give the rising civilizations more time to prove their worth, but this cannot continue, as the current harvest has already turned out to be too much of a fight for the reapers with significant losses.
Then, depending on the EMS value
high: Harbinger believes that the unification of all races that humanity and Shepard achieved, demonstrated in the suicide run on Earth, proves their worth. The harvest ends and the reapers leave the galaxy forever (maybe after helping rebuild somewhat).
medium: Harbinger is sceptical, the harvest ends, but the reapers announce that they will be watching...
low: Harbinger continues the harvest, the human fleet and their allies are destroyed.
Obviously needs some more work :-) But obviously we don't need to introduce a new character within the last minutes that resolves our central conflict in three alternative ways of which one does not make any sense and another contradicts everything Shepard ever stood and fought for.