I think the final battle of Mass Effect 3 will be a philosophical debate with Harbinger that's transmitted to every other Reaper in the galaxy.

You convince the entire species that everything they've ever done was totally pointless and thus, with their purpose lost, they self-destruct.
Seriously. I wanted to say something about the dark energy buildup and its effect on stars. I think this is in preparation for the next cycle. The CDN story about the TR-15 Letus Probe mentions "dark switches" on the mass relays that allow the control of radiation transmission through the mass relays. And the wiki has this to say:
Eezo is generated when solid matter, such as a planet, is affected by the energy of a star going supernova.
Energy, radiation, whatever. So, maybe the Reapers, after harvesting galactic civilization and most of the galaxy's eezo, blow up a few suns and spread the love through the mass relays to create new eezo for their next victims to mine?
And I've always preferred the theory that the Reapers began with an organic race continually upgrading itself through cybernetics and other means until it decided that being a giant spaceship was the perfect form of existence. And that everyone else should be that way, too. Plus, there was this one comment by Sovereign:
We have no beginning. We have no end. We are infinite. Millions of years
after your civilization has been eradicated and forgotten, we will
endure.
I've always interpreted this as meaning that the concept of Reapers, not necessarily the current species, is eternal. There was the Antilin ghost ship whose creators reached a similiar status entirely without Reaper interference (well, apart from the relays), even though they did so more out of necessity (at least that's what they're
telling people) and I think Sovereign meant that, even if his species is destroyed, other civilizations will eventually turn themselves into new Reapers and thus, the cycle begins anew. Anyway, I'd be disappointed if we got a definite explanation of the Reapers' motives and it amounted to "They're crazy/off their meds/malfunctioning." I'd prefer them to act out of genuine and sincere belief in their ideology, something like them being the custodians of the galaxy who wait to see if evolution churns out something useful by itself, then take and perfect it.