How did the reapers never fail a cycle

Unlikely they were able to fully survive a reaping.  You do have in the current listing 2 instances of of Protheans surviving the reaping.  First is the small crew that managed to survive long enough to alter the Keepers on the Citadel, and the second was Javick

Both show why this doesn't happen often but also illustrate the issues faced after a reaping.  One, since the Reapers are machines, they don't get bored or tired of doing this, they just harvest planet by planet going very carefully using all the data about the races there found on the Citadel.  Each planet is isolated because the Reapers control the Mass Effect gates so they can't really leave a run any great distance away.  IF you have a smidgen of warning, you may have a secret base NOT listed in the files, but then you run into the second half of the equation, time.  Ios lets you know it takes many many years to do a Reaping, we don't know how long, but it could be 50, 100, 200 years...longer??  So having a secret planet it would ALSO have to be self-sufficient also, and that is unlikely to happen, because think now, how well would your local town survive if ALL outside contact was gone.  No outside electricity, water, gasoline, material to repair anything except what was mined, grown and made in town, this is what happens when the Reapers come in. 

So between the length of time to Reap a civilization, lack of resources, all the info on inhabited planets, further info gathered from Husks and indoctrinated people, and the machine nature of meticulous harvesting, greatly reduces the chance of any real carry over of a civilization.  Because honestly, if one did survive, then it should then be able to break the cycle because they would have 50k years to prepare for the next cycle and build defenses.

There were survivors in the few first cycles maybe. Or so I'd assume. I don't remember exactly but it is said or heavily implied that the Reapers built both the Citadel and the Mass relays. They learned from their mistakes and even though they are machines with nothing but time on their hands they made sure every single species who made it to some kind of space era would evolve the way they wanted and would end up being easily harvested (or at least things would be made easier). We do have an example in the form of Leviathans of a species capable to survive not just one but many cycles (creators or not things are the same for them and every single other species, they are harvested).

If you think about the Reapers objectives, I doubt they would make planets inhabitable maybe a couple per cycle when the ennemy is kinda "too tough" (I think I read about it being done during the Protheans extinction but I'm not certain) but those planets would have time to get back to a state where they will be able to support life. So they'd poison the water or whatever but I doubt they'd go all Death Star on the planets.

Plus the number of surviving members required for a species to be able to live on is wildly different from one species to another. Take the asaris, you'd just need one single asari to survive for the species to survive. On the other hand humans would need several thousands souls (it's a guess) to be able to maintain an healthy population with a diverse pool of genes. Plus, when you say that the survivors and their children would have a headstart in developping themselves I'm not so sure. Here you have two situations either a groupe of random humans (let's take them) survived on some remote colony world. They will be able to tell their children about some things, what they witnessed and so on but will they be able to build a spaceship ? Or some kind of computer. Sure they'd probably have some remnant of technology but picture this tomorrow the world as we know it ends, everyone who knows how to do specific things like computer composents (or planes) died. We don't have access to internet anymore and nothing more than you little town library... We might be able to make some electricity (thanks science classes) but rebuild the internet ou computer might take a couple generations probably more. And I'm not talking about very scientific things.

Or you have something akin to what the protheans did. Selected people, representatives, the best in their domains are selected to become the weapon that will end the cycle once and for all. You might get back some level of technology faster but I'm not sure things would follow. Especially if we take our world for example. I mean... How many top scientist would be able to pass on their "superior knowledge"... And I'm pretty certain education would not be a top priority in the profile of people selected to rebuild humanity. Though, this depends wildly on the species and how they think.

It is possible that the Reapers used some kind of Collectors before making them to start harvesting species or to finish the harvest.

It is also possible many species lie in sleeping pods buried deep underground as their final resting place because they too wanted to do something like the Protheans but ultimately they failed. And cycle after cycles they were uncovered and then erased. And they might also have survived but not in sufficient number for their species to live on and/or the tales of the ones that survived the Cycle became some kind of legends no one in their descendants believed and thus the Cycle took place.
Because yeah it's nice to say "they'd prepare themselves" and all but... 50 thousand years would pass... They might start some highly disciplines war focused species but do you see humans stick to such way of thinking if it is not in their nature ? Plus they might become kinda like the Protheans, an empire doomed to fail.

Now crazy thought if there were always some survivors in the Cycles, just enough to uplift a couple species before disappearring ? What if the Reapers actually never failed a Cycle because they made sure the cycle would evolve as intended using former species to that end (wich they kinda already did with Collectors). Or it's actually the same species being harvested over and over again but with only the dominant species (or the one that intrigue them the most or whatever) being completly harvested with some kind of alternating evolution between some species like Humans, Asari, Turian and Salarian on one cycle, the next Krogan (Salarians uplifted them that's why I'm putting them here) and the Yahg on the other. And because they are beating back species to the dark age there is only some tales left of their harvesting.

I actually loved reading all of that :O made sense to me the whole way. 

Your last part reminded me of a story in Mass Effect 1. Im pretty sure there is a planet with a prothean artifact, a big floating ball or something and it revealed a story from an ancient human's perspective. I think it involved him feeling like he was being watched, having a pain in the back of his neck (presumably from a tracking chip) and him seeing a ship in the atmosphere. 

I think the chip might have been done by protheans but for some reason i remember picturing the ship he saw as a reaper checking if humans were spacefaring or primitive. Imagine if you were right and he was a human version of a collector and couldnt remember the reapers harvesting them and he was left with his tribe to repopulate :O

Although that would honestly kind of go against the reapers whole thing of a natural cycle of the galaxy if they were manually recycling species. Would be cool though of dinosaurs were actuall an advanced race that the reapers harvested and humans found their fossils :P

I'm happy that you enjoyed the read and that it made sense x)

Yeah, the last part is a crazy thought I got. There are probably a few dozens reasons why it cannot be so x)

I do remember this moment. You activate it with some sigil or whatever Sha'ira gives Shep. Thought if we remember the way Protheans communicated and the fact this communication goes both way (Javik reads Shepard and can speak in the current language used in this cycle while Shep sees some part of the Prothean extinction). We can assume at some point in time Prothean scientist observing humanity incerted a chip or whatever in this human (or collected some data) and received this moment as a "transfer" and somehow stored it (remember Javik memory shard) to further analyse it.

Though the idea of the ship being some kind of Reaper or Reaper scout could be interesting not only because of dinosaurs x) but because if you think of this memory as some Prothean who stored it you kinda have to ask yourself "why would they store such an uninteresting memory ?" well if you have something they do not recognize or understand in their vision that might explain it. They stored it as a reference or some kind of a wanted poster thing or simply just to signify their people a new species was there to be absorbed by their empire. Only realising way too late that they saw the first ship of an invasion.

Plus, if you think of the timing that might be the moment reapers started harvesting Protheans so they might have seen in the Citadel log that Protheans were monitoring Earth and wanted to make sure they could not bring a new species to the fight.

Not sure about the "more intelligent species than before".

Listening to Jaavik I understood Protheans actually were composed of several species (wich by being either beaten in submission or agreeing joined the Prothean Empire and thus became Protheans). The difference between the prothean cycle and the Shepard cycle is more along the line of how different species worked together. By all being Protheans and following a single ideology the Protheans became vulnerable once their tactics or whatever were analysed. On the other hand we have the current cycle wich is more about cooperating species working together to be stronger. Each species keeps their individuallity, their strength and weaknesses, alone they would have been quite easy to destroy. But together they somehow compliment each others strength and weakness and thus are able to stand a bigger chance.

That being said... We don't know for how many cycles Reapers have harvested... There were at the very least four cycles (Keepers, Prothean/Collectors, Leviathans and the one you play) but for what we know there has been much more cycles than that. So it would be somehow "logical" that you'd find two cycles where the political situation was the same as the one we encounter during the events of the game and a big number of advanced species. Maybe in some of those cycles there were more species thant in the one we know.

What makes the difference is based on so many different parameters. It's at the same time Shepard receiving the warning, to some point Shepard who is able to unite every species to the fight and assured the loyalty of quite a lot of key people. It also is the fact that Shepard and everyone got the tech from the previous cycles destined to end the Reapers once and for all.

And yeah, you can argue that for what we know only one species got "elevated" as the Reapers minions (Keepers and Collectors). But ME2 kinda makes a point about the Reapers choosing the species they want to keep and simply erasing every other. And even if you think about what Sovereign says it does not imply a small number of intelligent species.

This one is probably the most accurate tbh, i brought javik for most missions in my current playthrough and yeah there is a lot about how the protheans were an empire that dominated and brought weaker species into their empire. They were basically the protheans and all the races that lost to them and adopted their ideologies in order to survive. species that refused to follow the prothean way of life and join their empire were wiped out. 

That was also their weakness, when the reapers figured out their strengths and weaknesses it applied to their whole empire because all races were following the protheans. In the current cycle all the races maintain their own strengths and weaknesses and work together. 

I feel like realistically the reapers would have made a new capital ship out of all the main species and smaller ships out of all the lesser species. So in the current cycle i reckon asari, turian, salarian and maybe human would be capital ships because they are council races or whatever and then all the smaller species would become smaller ships, so the hanar, elcor, volus. 
The drell just have no chance xD not enough of them to be turned :P