Part one of … not sure
The following is just a couple ideas of how things could ‘be’ after the events of Mass effect 3 – despite the bad ending… 😉
Since there are a lot of things not actually ‘shown’ in the final cut scenes we are left to wonder about a lot of things like what happened to some characters, planets, technologies etc.

My preference for the ending is of course the ‘destroy the Reapers’ option.

First off – a couple of things that can be directly deduced from the final cut scenes:

Some characters definitely (from what I can see) survived – like Joker, Liara, Garrus, Ashley/Kaiden, the Prothean and Admiral Hackett. Possibly Tali, Grunt, Jack, Jacob, Zaeed, Kasumi, Miranda could also have survived. I’m a bit unsure about Wrex since there was a cutscene just before the ‘run to the beam‘ scene where he and some Asari commandos were hit directly by a Reaper beam. Most of these characters would have been on the Normandy when it crashed (but I’m still totally confused how they managed to get back to the ship at all and why!?). They would be stranded in the middle of nowhere between points where Mass relays were. That implies they would be nowhere close to any known planets or space traveling routes which implies no one else would know where they are as well. Sheppard is almost surely dead unless that secret ending hint is true (only possible if you choose the destroy option with very high war readiness). Anderson is dead – period. So is Thane and Mordin.

Most the major civilizations home planets are destroyed – except for Sur’Kesh’s (Salarian), Rannoch (Quarian/Geth) and Tuchanka (Krogon) (which is a wasteland anyway). To be specific the planets Thessia (Asari), Palaven (Turians), Dekuuna (Elcor), Kahje (Hanar and Drell), Irune (Volus), Khar’shan (Batarians) and of course Earth are destroyed or very close to it. There may be survivors but the best chance for survival would be small colonies that might have been secondary targets for the Reapers which they would have attacked later if they survived. To summarise – there are survivers but they are spread all over the place and isolated. Many small colonies might actually die if they cannot survive on their own.

Although the relay network was/is (tenses are gona be confusing since I refer to fictional stuff here) disabled or destroyed depending on ‘Sheppard’s choices travelling between major planets are difficult if not impossible in a reasonable time. There is a posibility that some could have survived – those that has not been activated, discovered or disabled in the past. Even so the network as a whole would be out of commission for all practical purposes. FTL drives would still operate but since most technologies were based on the relay network most civilizations would not have bothered to make advances in FTL technology for very long distance travel. Even if they try it it could take years, decades or even centuries to travel to other systems – especially those that are on the other side of the galaxy. Think of the poor Quarian fleet that have to travel back home (provided any survived the final battle over Earth). Then again they were ‘used’ to long term space travel so perhaps… If any Turians or Asari ships survived they would also have a very long journey ahead of them. The same goes for Krogon which probably have to hitched a ride with the Asari since Tuchanka is on the way to Thesia as seen from Earth.

Pockets of small fleets that might have been traveling or battling Reapers in remote locations would also be stranded. It is assumed that most of Earth’s forces were at the final Earth battle so these pockets might mostly be those of other species.

The Citadel is destroyed or very badly damaged. If anyone survived the Reaper take-over they probably would have died during the final ‘beam’ event. Still, it is a massive structure so perhaps parts of it could have survived or could be re-used for rebuilding something else.

Other technologies might also be affected. During the final conversation with the Catalyst (ok more like a monologue) it is stated that some organics already contain some synthetics. Whether that means they also would stop working given the destroy option is unsure. The same might apply to the ‘control’ option as well. With the synthesis option those technologies obviously will survive. So the general feeling I get is that technologies like biotics and Mass effect type weapons would still be usable.

Deductions and theories.
So how could things change given some time of recovery? Although the Earth’s surface has been all but destroyed the survivers have access to all the element zero formally used by the Reapers. That would give them a good chance to recover more quickly. Perhaps the same would happen on Thesia and Palaven as well. Using the larger concentrations of element zero some more advanced FTL drives can be developed.
Humans are adaptable and if (real) history teach us anything even major disasters can be overcome as long as there are a few survivors. The biggest threat (other than surviving Reapers) would be pirates that would also be desparate after the whole invasion. They would strip any resources they can lay their hands on. Actually, any survivors would fall into this description.

One theory or idea I have is about whether any Reapers might have survived the ending – given the destroy option. If it was only the blast from the Catalyst that killed/disabled them then there is a chance that some might have survived in deep space away from the relay network. I don’t believe they would have sent all Reapers to the final battle over Earth – not even an AI would be so foolish to take the chance that some enemy can potentially wipe out all of them in one single battle. Also, given their long history they more than likely have multiple hiding places.
Then if the Catalyst merely used a signal to disable them why would the all willingly simple ‘kill’ themselves? What intelligent being would willingly self destruct just by getting a signal? Some could have rebelled or refused to obey. This is all speculation but it does raise one big problem. If any of them did survived the organics would still have a major problem! Being almost wiped out, many isolated or spreaded thin it could only mean the Reapers would still have won and can clean up the survivors and then start rebuilding for the ‘next cycle’… This is one of the reasons I don’t like the current ending of the game – by removing the relay network any further resistance would also be useless and destroyed.
If Sheppard choose one of the other two options then the Reapers definitely would have survived. On the Mass Effect Wiki it is stated that the Reapers then ‘peacefully’ leave the galaxy… but why would they stay away if they need to harvest organics to survive themselves?? A predator cannot stay without food forever…

Another totally different idea I have is – what happens in other galaxies? Do they also have Reaper like ‘control’ mechanisms to avoid synthetics from destroying organics? Even if the Reapers in the Milkyway do get destroyed how long would it take for such ‘alien-reapers’ to realize the vacuum of power in this galaxy and come over to prey on/help organics? Then again it was never stated definitely that the Reapers are ‘only’ from the Milkyway. They could even be from another galaxy for all we know.

Yet another idea is what is the posibility that some civilizations somehow did not encouter or refused Reaper tech? They would then develop on their own – slower but without the influence of Reapers. How would they fit into the bigger picture? Such a group could develop tech that could be unknown to the Reapers and possibly have no defences against. Of course they might have the same issue with developing AI’s that may rebel but there is also the posibility that they survive or sidestep that problem. However, such a group would not fit into the Mass Effect universe at all and thus could be ignored – sorta.

Given that Javik survived and he can read/talk Prothean he could help with technology discovered at Prothean ruins. They were alway presented as very advanced and the ability to understand such discovered tech could be very valuable. The problem is just that he and the rest of the Normandy crew are stranded somewhere out ‘there’. Just imagine Liara and Javik conversations about discoveries she made – during all that time they are stuck on that alien planet… but Javik might actually get crazy of it all 🙂

If Sheppard and Mordin managed to create and spread the cure for the genophage the Krogon would again thrive on their planet, despite the conditions. This is one good reason for the relay network to be disabled. The Krogon could then only expand to close-by systems when they start expanding again. A problem would be if Wrex did not survived (which I suspect). This would mean the Krogon would once again fight among themselves but at least it would stay ‘local’ only on the planet. I kind of felt sorry for them in that situation.

The Rachni is one of those possible good and bad things depending how they turn out. If any of them survived the final battle they could possibly be a problem on Earth because of their past history and the misstrust between other species and them. Thankfully Sheppard didn’t bring a thresher maw along as well!

So what would happen if among the debries of the destroyed Reapers they found plans or notes on how to build a new relay network? That could be a very interesting avenue for a future direction for the Mass Effect universe. Even if they did find tech like this it would take very long to establish a new relay network as you have to first travel to the destination manually to build a ‘destination’ relay before anyone can jump to that point. Even then you have to use ‘local’ resources at that location to build that relay. This makes me wonder how the network was built in the first place and how long it took? Certainly some ‘old’ gates as mentioned before could still be there – ones deactivated, burried or disabled that can help to spread the new network again. Would this be a good thing? Who knows? At least if the network between the major civilizations could be restored it could help a lot. There is also the chance that the Reapers themself did not actually create the relay network but inherited or conquered it from someone else. Perhaps the ‘gate/relay’ builders still exist somewhere in the universe or they were the first victims of the Reapers/AI’s.

Catalyst is lying idea

I’m sure I’m not the only one that has thought about this idea. Given how powerful mind control abilities the Reapers (Saren) had it is not unreasonable that everything the Catalyst supposedly said could be a lie to accomplish something else. Also seeing that the relays, Citadel and lots of other technology were actually ‘theirs’ it is not hard to imagine that even the Crucible was actually their design just waiting to be discovered and used by organics to do their bidding. They could have used the attack from the combined fleet from the organics to simply get all remaining resistance in one place to wipe them out in a single battle. It would be a terrible tragedy that Sheppard played right into their hands (perhaps under their influence) – ironically and unknowingly following the same path as Saren. Just perhaps that is why the Normandy was running away from the Sol system… to get away from the influence. If so hopefully they took Sheppard’s body along as well that might still have been laying next to the beam dreaming the whole encounter with the Catalyst… (One issue with this idea is that was Sheppard;s actions that let to the Relay network destruction which stranded the Normandy so how could the crew have Sheppard with them while they crashed… questions, questions, questions…)

This might open the possibility that there could be a continuing story involving Sheppard somewhere (but BioWare did state that this game would/should be the last involving the character… but… they could also be lying like the Reapers hehe).  Perhaps we’ll have to wait for part four of the trilogy (Mr Douglas Adams would have been proud 😉 )

But these are all just ‘what if’s’…