I'm the opposite, I think the whole Catalyst AI who controls the Reapers because he doesn't want synthetics to kill people so uses synthetics to kill them all so they don't get killed by synthetics, and then giving the choice of Destroy, Control or Synthesis is just the most ridiculous, out of place ending I've ever seen in a narrative. Realistically, sticking to the themes of all 3 games up to that point, it should have been a conventional victory. If Destroy was the only option and the Reapers weren't controlled by some crazed AI that has pulled you into some weird dreamscape, I might have been a little more behind it, but adding space magic at the end just made me want to throw the damn game out the window.
Over time (I used to be quite anti-ending, now I'm considerably more pro-ending), I've come to realize that the general understanding of the Catalyst and its mandate here makes a case that is underlined by an appeal to common sense: As in, people like to call out how the Catalyst chooses to enact its own mandate in a somewhat paradoxical manner, using synthetic machines to periodically purge life from the galaxy to prevent organic races from creating synthetic machines that will inevitably purge those races from the galaxy.
The difference is that (and yes, heavy speculation here I admit) the Catalyst is a so-called 'meta-stable' intelligence that has transcended the issue by understanding the concept of restraint. It has a mandate to fulfill, and that is to prevent the permanent extermination of all organic species in the galaxy. The Catalyst does not permanently destroy everything. It purposefully leaves organic races with the ability to recover to repopulate the galaxy, reach the zenith of their culture, then bring them down to prevent them from developing their own life that they would inevitably lose control of. Now, you may argue that this was the case of the Leviathan's race. And technically, you'd be correct. However, that race was sufficiently advanced enough that the AI they had created was able to recognize an inherent flaw in the mandate of the Leviathan's, and was able to circumvent this by creating the cycles to prevent the permanent annihilation of life. It's why I'm able to understand and even technically agree with the Catalyst's mandate; it's perfectly logical and rational. The issue is that the mandate in question is irrelevant and presently incompatible with my goal. While I do agree and understand the Catalyst, that does not mean that I agree with the present actions of the Reapers it leads. Their current goal is incompatible with the success, prosperity, and survival of my own society and goals. So I set aside the mandate as a problem of thought for now to be dealt with at a later date and solve my current, much more pressing issue of defeating the Reapers and insuring that we have a future to face the Catalyst's mandate at a more convenient time. Granted, I wish I had the ability in the game to vocalize this. It's why, while I've come to terms with the ending and its overall picture, it's still a narrative and executional mess that sucked donkey balls.
As well, I honestly do believe your stance belies a lack of critical thinking on your part regarding the themes of the series (which are not obligated to be 'fulfilled', so to speak, by the ending). Perhaps the ending was unforeseen, but I no longer believe that it was out of place. It was very much out-of-the-blue and alien, but I believe that was the point. You're finally seeing the accumulation of all your efforts and find that the entire issue is based on the the blue and orange morality of an unforeseen entity that is not and does not need to beholden to your own views and ideas of the themes.
I'm not trying to insult you (and I apologize ahead of time if this seems to be the case here). The themes of a series are a metaphysical recognition of, well, themes by the external audience (the player), not an ingrained part of the narrative or lore, nor are they physically manifested or existent in the setting or the lore. The themes exist outside the games, not within them, and we the audience view said themes, not the characters and agents of the narrative.
On the other hand the setting and the lore are all internal and physically manifested within the narrative universe; and this lore has decreed that the Reapers are indeed far too powerful of us to even contemplate winning a large-scale confrontation with them. There is, quite simply, utterly no chance in hell of us ever being able to beat the Reapers. They're simply too powerful and too advanced.