Develop original ideas. Remember Tali's mission in the ME2? A star was aging too fast. So the idea (before Drew Karpyshyn left Bioware) was that using eezo caused fluctuations in dark energy that affected stars. And if it's not used everything stabilizes. Sub-light communication and transportation demand eezo. And a lot of eezo is used before inventing sub-light transportation. So, the thing is Reapers built mass relays in order to lessen eezo consumption. Either way, one race or more would invent sub-light messengers and transportation but they would consume tons of eezo before it and that's why stars in the Galaxy would be aging. SO, Reapers don't harvest just for lulz (and to prevent synthetics vs organics wars lol). They allow peoples to try sub-light much earlier in order not to let them use eezo before. They let them skip a step of great consumption before inventing mass relays. All the cycles Reapers try to invent the sub-light transportation that wouldn't affect stars in such dramatic way. And hence the ending of the 3rd part would be: 1) You destroy Reapers and condemn the galaxy to quick destruction. 2) You sacrifice yourself to give hope to the future peoples of the galaxy. And the 3) option. You destroy mass relays and everything that demands eezo. You deprive yourself of sub-light motion in the hope that someday another variant will be invented that does not imply the use of the element zero.