Well, the Reapers keep spouting their drivel about being the "salvation" for organics.
So, their perception is that they save the organics for something. The reason stated in the canon is the creation of synthetic life that ends up destroying organic life.
However, that alone is oxymoron; life is life, synthetic or organic - there is no fundamental difference whether the molecular machinery is running on naturally evolved chemistry, or intentionally designed one, and similarly it doesn't make a difference whether the being is controlled by an organic neural network generated consciousness, or a true AI.
The Reapers' logic seems to be this:
1. organic life will eventually create synthetic life, if allowed to develop it freely
2. synthetic life created by organic life will eventually rebel
3. synthetic life created by sufficiently advanced organic life will end up uncontrollable by its creator species, and, in worst case, uncontrollable by anyone or anything
4. synthetic life will for some reason be motivated to destroy all organic life
5. to prevent destruction of all organic life, synthetic life must not be allowed to be freely developed
6. to prevent the free development of synthetic life by organics, the organic cultures must be periodically stopped so that they do not advance far enough to create unstoppable synthetic life
7. to prevent the destruction of said organic cultures, they are harvested instead of being destroyed - the harvesting could, in a way, be descrived as "archiving" the species in Reaper form.
Of course, this logic has several flaws. First of which is the base assumption that synthetic life will inevitably destroy organic life. The game tries to address this at one point where EDI poses a question about the meaning of synthetic life, but fails to follow-through on it, especially with the later evolution of Geth to become true AI's. So, we are not given any actual proof that synthetic life will always attempt to wipe out organic life; in fact we are given evidence of contrary, that synthetics and organics can live in co-existence or even symbiotic relationship.
Secondly, there is no explanation as to why synthetic life taking over would be an explicitely bad thing to happen. When there's no functional difference between synthetic and organic data, what then is supposed to be the difference? I for one do not see one.
So, in their determination to solve a "problem", the Reapers have become a much bigger problem themselves. Instead of allowing the galaxy to evolve freely, on either organic or synthetic route, they are effectively enforcing a level of stagnation where no space-faring civilization can be much older than 50,000 years. While a long time for a civilization, this is not especially long time in evolution of species. That basically means that the species capable of forming space-faring civilizations must already be pretty well evolved at the time of a purge in order to participate in the galactic civilization of the next cycle.
Additionally, as a long term solution, the Reapers are a piss poor one. At some point, they will run out of new species to harvest because the prominent sapient species from all the planets within the Mass Relay network have been eradicated and new sapient species have not had the time to evolve. What will they do when they have harvested all the species?
At that point, synthetic life has, basically, eradicated organic life and taken over - an occurrence the Reapers specifically claim to be designed to avert, according to the Citadel AI.
The interesting thing in Mass Effect galaxy is that there could be millions
of relay networks equal in size and distribution to that connecting the Humans, Asari, Salarians, Turians and all the other species shown in the series. There could be thousands of galactic civilizations, working on overlayed networks but never gaining contact with each other. The Milky Way is 100,000-120,000 light-years in diameter, and after discovering the Mass Relays, a civilization would have little use for powerful radio- or laser communications limited by speed of light, when they have a convenient FTL communications and transportation facility at hand.
The Mass Effect galaxy is far, far too small to depict an entire galaxy of species, and it is my belief that the network of relays known in the game is only a small fraction of what is going on in the entire galaxy.
It is possible that the original Mass Relays were constructed by a single species that put them in places they deemed probable to produce life - it might explain the high ratio of habitable planets on the systems known in Mass Effect, almost every system has at least one earth-like planet on goldilocks' zone (with atmospheric pressure and temperature allowing the existence of liquid water).
There could be other relay networks, either built by the same species, or possibly built by other species utilizing the same Mass Effect technology.
Perhaps the Reapers themselves only "police" a small fraction of the galaxy - the area connected to the specific relay network constructed by the original species.
Then there is the question whether the Citadel was built by the same species as the Mass Relays. Although I doubt it has been stated anywhere, it seems a logical assumption that in canon, the Citadel, the Mass Relays, and the Reapers were all the product of same entity.
Further speculation from my part is that the Crucible was actually part of the original design specification of the Citadel, rather than an "add-on" designed by subsequent civilizations. Or, to be exact, the design specification for the Crucible was likely left behind by the original species, and later found, adapted and worked on by other civilizations until it reached its form seen in Mass Effect 3.
Its capabilities and basic functionality (such as how it interfaces with the Citadel) need to be determined; in the canon it is capable of the following remarkable feats:
1. Destruction of all synthetic life, reapers included, but somehow capable of differentiating with normal machinery and construction
2. Subjugation of all synthetic life to a deceased person's will
3. Combining all living things, organic and synthetic, into one entity of combined organic-synthetic beings that evolve using a "new DNA", whatever that's supposed to mean.
None of these options either make sense or are especially appealing to Shepard or the player, considering that two of them spell certain doom for the main character and the third one offers only a slight chance of survival depending on how much effective military strength Shepard has under control. This will likely deter many players who don't see any option as a "good" ending; I confess to being one of them. But, death by heroic sacrifice is of course a valid way of writing off a character, so I can understand Bioware doing this - except for the Conan Doyle sight of Shepard taking a breath at the Destroy ending if you have enough points...
The bigger problem for the Mass Effect universe is, obviously, the destruction of the Mass Relays themselves. There is no longer a convenient FTL comm and transport structure in place to funnel civilizations to Citadel (which also is destroyed as far as I could tell), so they are left to their own devices for untold amount of time. Building a relay network takes significant amount of time if you have to move from point A to point B at slower speed, and construct the relays at every relevant point.
So, what I see the ending having is:
-viable option to keep Shepard alive
-option that doesn't involve categoric destruction/subjugation of all synthetic life
-option that doesn't involve destruction of the relay network and the Citadel
All of these would seem to require modifications to the canon behaviour of the Crucible, most crucially, but adaptations to (or removal of) the Citadel AI are also needed. My hypothesis is that all the three modes of Crucible action utilize the energy source and relay connection provided by the Citadel, and the Crucible merely provides means of converting the energy to desired effect by magitech handwavium.
Part of the energy is released in an initial burst, and part is directed to the relay network, whereupon it causes each relay to release their energy and to convert it into the effect desired by the Crucible activator.
Matth's suggestions about using the Crucible to disrupt Reaper communications (including indoctrination) sounds viable; it could be explained that the Crucible device makes each Mass Effect relay prevent Reapers from using their communications within typical short range FTL flight range of the relay itself, so that would make the systems themselves safe from indoctrination.
This option would do nothing to the individual Reapers' capabilities in space, which is where they have proven to be the most effective and dangerous opponents. They could also reasonably easily adapt to the comms warfare - but implanting their minions with communications systems that use less easily disruptable means of communicating.
Other options would make the Crucible-Citadel some sort of Death Star (we all expected something like that, didn't we?), or some of the more drastic means of survival.
The Crucible could be a cloaking device - pack up the Citadel and hide it somewhere along with the assembled fleets. It could also double up as a warp drive of some sort, for additional range if required.
These are the voyages of the Starfleet Citadel.
Its continuing mission: To explore strange new worlds, to seek out new life and new civilizations, to find habitable planets for all the species in it; to boldly go where no member of galactic civilization has gone before.
Battuta's option about blowing the **** out of Citadel itself sounds oddly appealing, even if it ends with a failure as the Reapers just shrug it off and continue harvesting. Maybe the Crucible could be used as a bomb to destroy the citadel internally, by attaching it, then closing the arms and detonating it within - perhaps shielding Earth from the explosion but destroying all the relevant hardware inside the protective arms.
EDIT: Someone mentioned the Dark Energy foreshadowing in #HLP-ME3, and Swantz posted this in the other ME3 thread:
It would certainly be a more compelling motive for the Reapers than the stuff they were given.