SO the theme of Mass Effect is "Accepting another's path blinds you to alternatives" 
Oh, this would have been so much better...
Just imagine: the Crucible is presented the same way it is currently, but there are alternatives that are only hinted at and are hard to get, and their effectiveness depends entirely on your choices.
(For example, if you spare the Quarians you can use a modified version of Xen's grenade to temporarily disrupt the synthetic portion of any Reaper, which leaves the organic part unsustained and thus kills it, leaving the targeted Reaper an empty shell that maybe can be controlled by other Reapers... or by the Geth, if you spared them too and persuaded Quarians and Geth to trust each other and fight together this way;
another thing I can think of at the moment: you could give all the info available on the Reapers to any known pre-space civilization, along with most of the available tech schematics and a sensor that signals when the Harvest is done; this way there's hope that the next cycle will develop a way to counter the Reapers, and will do so fast enough to actually stand a chance... by for example disabling every Mass Relay just before the next invasion, and developing high-precision extremely-long-ranged artillery and sensors that make it possible to pick off the arriving Reaper fleet before it gets in range to actually fight back).
Yet the Crucible is the only one made obvious, and presented as the best and easiest.
But in the end, it's also the only one that does
not work... and maybe it's revealed that its plan is leaked by the Reapers themselves in each Cycle, so that the races will waste their resources and time building it instead of actually resisting and blind themselves to any alternative there may be.