That´s the problem, if you´re taking literal version for what it is, then Crucible was created to not just being some sort of battery, but to power up something aboard of Citadel, which brings lot of questions. If the Reapers were always successful in their surprise attack, then every cycle end up with disabled relays and no chance to not just deploy the crucible, but even to develop that thing. The answer is that someone else had to mess with Crucible, to even bring a plan of it to cycle that has no knowlendge of Reapers or Catalist or Leviathans.
The harvesting of a cycle can take a long time and they could still try to build the Crucible, but yeah, being surprised like that they still had the disadvantage which led to their failing. We know from the Protheans that they started building it but never finishing because infighting broke out due to indoctrination.
I assume each cycle always hoped for the next cycle to do something about it, and at least tried to hide the plans as best as they could from the Reapers for the next cycle to discover.
And sure, the Reapers disabled the relays in every cycle before, and the only reason this didn't happen to us was that the Protheans were smart enough to help our cycle, and even that was a very close one because no one believed in the Reaper threat. But this is the chance I guess many cycles have waited for.
I'm not sure what exactly you're referring to by "power up something aboard of Citadel". Powering up something would be in line with the energy the Crucible creates.
Indoctrination is being missunderstood quite frequently, it´s not about that Shepard was already indoctrinated, but about the process of being indoctrinated, thus Vendetta has said that indoctrination is not detected, but not the process which is entirely different thing. If you connect the dots, Rachni - dreams and indoctrination, then you´ll end up with conclusion that Shepard is simply in the process, and at the end of game you are having a choice betwen the joining the Reapers or being free of their influence, or even able to refuse to do anything at all.
Shepard was for years walking around the Reaper technology and he didn´t have the vision, not till the Arrival and after the start of invasion, whatever TIM did installed himself with, it seems that it gave him power to control, to manipulate Shepard´s body and will, which is strongly tied to indoctrination.
Still not buying it, sorry.
What TIM did was likely tied to his research at Sanctuary, it doesn't have to do with indoctrination, but truly control someone. There are even powers like that in the game, Dominate can do something like that.
I feel that with the EC slides, which directly show that you've actually shaped a future in all of the game's outcomes, and the dev tweet that confirmed Shepard is on the Citadel, I have even less reason to believe in IT than I did before (I played without EC first and never once thought Shepard was indoctrinated, I only read here that it's a thing). People can believe anything they want, I'm fine with that, but that will not convince me that IT is true.
The thing is that destroy ending was most disregarded by Catalist, he came with this supposed conflict, even if you encounter AIs that is not so happy to kill organics, and your whole jorney changed in one second from killing a Reapers into stoping some endless cycle of AI vs Organics.
Rannoch's truce doesn't prove anything imo. Each faction wants something and they both get it by playing nice... It's the same with the whole galaxy being united by Shepard, they all just do it because they face a common enemy that would wipe them out if they didn't all work together.
The Catalyst works with an equation from Leviathan's programming plus the data it gathered during Leviathan's time, so it always sees the organic-synthetic problem as true according to its logic.
I generally get rid of the Catalyst and the Reapers, but not because I think the Catalyst is wrong about the past, but because I think the races don't need something dictating their fate for them.
And how did your journey change? You can still kill all Reapers if you want to. And the cycle has always been a thing since ME1, so yeah, of course we deal with the cycle, we just didn't know the reason for the cycles up to this point.