User blog comment:Legionwrex/Why Destroy is the worst ending (besides refusal)./@comment-5236409-20120709155811/@comment-127338-20120709171224

Arbington main issue with defeating reapers was time- Galaxy did generaly have reasources to nail down even Sovereign class reaper.

On Palaven they actualy proved how easy it is... just smuggle a nuke or warp bomb onboard and Reaper is toast.

As they put it an FTL projectile which would drop out inside reaper would easily destroy it no matter it´s shields or plating... but general FTL technology avaiable to galaxy had built in safeguards agains precisly such use (which btw are most likely Reaper in origin too) ... and there was neither time, nor resources to rebuild it from scratch in sufficiently massive quantities. It would simply not engage if it detected object in path or at exit coordinates. (Which I am sure could be worked around... but it would take time... easiest would be to fool it by running sensors in loop and aiming ship manualy.)

Plus another issue- such weapons were generaly outlawed by all pre-reaper invasion conventions of war... so...

It is mentioned in "extreme measures" codex entry, or something like it. Reapers are not that hard to destroy once you either break through, or bypass their shield... in fact single resonance torpedo did the job once Sovereign´s kinetic barriers were down in ME 1.