About the rebellion part, yes, but not about the "synthetics will wipe out all organic life" part. For that, it would have had to wait a lot longer, it would seem.
Oh, sorry, I didn't answer to that part, true.
While you're correct of course, I think this can be tied very well to its equation that synthetics always must surpass their creators, and that this means inevitable conflict. That it acts before a species is forever lost to the conflict. Is it premature? Yep, sure as hell. But seeing how the Catalyst is something very different from us, it has different ideas, views, and yeah, maybe even experience. We also don't know what else it tried before, just apparently a lot of different things, and the harvest is the best it came up with for now. I'm curious about its other tries.
Ugh, "zha'til"? Maybe I should try to look that up somewhere...oh, here it is: http://masseffect.wi...Races#Zha.27til.
Hm, there doesn't seem to be anything about the zha'til that indicates a sudden evolution of synthetics who then...you know.
Okay, I've dug up some more stuff, and apparently you'll get this line if you take Javik on the Dreadnought with Tali:
Javik: "In my cycle, a race called the Zha used machines, the Zha'til, as synthetic symbiotes. The Reapers subjugated the Zha'til as they have the geth. Their mechanical swarms blotted out the sky. They were brutal, merciless."
Of course, this only says what happens after the Reapers arrive, before that, the wiki states:
At some point, the Protheans encounter a hostile race of machine intelligences that endanger their existence. To combat this threat, the Protheans aggressively assimilate many other spacefaring organic races into their empire. The Prothean Empire is able to fend off the machines in a conflict known as the "Metacon War".
So... we know they're hostile, but not if they truly took over the organic body. It says "machine intelligences", which might suggest the organic part was long gone? Or maybe they just truly lived in symbiosis until they meet another race in form of the Protheans and felt threatened or so. We can only guess it seems. Or take the Catalyst's word for it 
It started the first cycle after studying the thrall civilizations of the Leviathans, so maybe further observation wasn't necessary.
I think the 50k year cycle is just another plot hole, because obviously one cannot predict the evolution of civilizations within such a time frame - the current cycle starts thousands of years after the current advanced civilizations are able to build dangerous synthetics, but without any indication that they are planning to do so, with the exception of the Quarians of course.
So, well, I think that the motivation of the 50k interval is simply unexplained and unexplainable, ergo: plot hole.
Could also be, maybe it thought it had enough evidence from the Leviathan's cycle, it seemed to have happened a lot more there with the conflict. Who knows how long this went on before they had the glorious idea of creating this nice tool for themselves.
Is that really a plot hole? I mean, sure, it seems weird it's always the same interval, but we've seen more magical things happen, hehe.
That would maybe fit again with "you develop along our desired path". By strategically leaving behind tech to discover, it could ensure to develop the civilizations in an a bit more controlled way, and... Yeah... no, not really I guess 
Awww, don't throw around with good reasons, man! Reasons are for loosers, man! They always write novels about how it is not their fault, because of reasons, that everything goes downhill, and their dog gets killed, and their bible is stolen etc. etc.
Winner-Shepard is the one where everybody survives, and all are united and understand each other and live in peace, well, except for the reapers killing everybody but you get the point, and the Geth crawl inside the Quarian's suits without that being weird, and Shepard becomes prom-queen and wins the beauty contest at...no, wait, that was...anyway, you can make up what you want, the game itself tells us what is objectively best with its EMS score, except where it doesn't, and the wrong choice actually scores more because developers can't calculate despite working with a computer for god's sake! (hint: genophage).
I'm a loser baby!
I had Winner-Shep in my first run, was pretty neat. But it lacked drama
I love drama. I enjoyed my FemShep run who was the mission first type and did some serious questionable sh*t much more. It was intense for sure! Genophage arc was the best.
Yeah, I know what you're aiming at, but it also makes sense Synthesis is only available with high EMS (energy thingie and Crucible being largely intact). I used to see all of the choices as equally "best", depending on the player's reasoning. But... it really seems Synthesis was supposed to be their intentional best. Ha. It rarely gets picked (sounds like the poor squad mate during the Citadel DLC
).
What you mean with the genophage I don't know though.
I think it just sounds depressing...and actually the VI does not seem to be that different from Legion. But I notice that the writers designed the story variations so that gamers would find their previous descisions reinforced - if you distrusted Wrex and the Krogan in ME1 and ME2, ME3 actually takes a turn that vindicate this. Same with the Geth. Strange. Wouldn't it have been more interesting the other way 'round?
It was, haha. There might be tears (seriously, there were...), but I can take it! And really, Tali's reaction there was amazingly beautiful, it was so good.
I don't think the Geth VI was that different either, it's a good substitute. The only thing you're missing is the history with Legion and the possible trust you've built with him. But the Geth VI really is not that different, just... found that part interesting inside the Geth server. Made me think about their goals some more. In the end, like I said, you have to make up your mind what kind of Shepard you are 
You mean when you shoot Wrex and get Wreav instead? Wreav is a pr*ck, yes (I say it with Vega's words, hehe), but the Geth VI isn't.
I think you could also mistrust the geth previously, but then decide to trust the Geth VI. Everything can work. Because reasons 
However, you could ask the same question with trust in the krogan and geth. Wouldn't it be interesting to see how that backfires, maybe depending on some choices? Much like when you let the Reaper Rachni Queen join the war effort, that is some bad choice, hahaha. I guess it's implied too with Wreav in charge and a cured genophage. I don't know though if it's more positive if Eve is still alive.
And, yeah, "try this because it makes the Catalyst seem less stupid"? Not the best advertisement 
Hm.
"Fraggle script doctors inc. Hurting after your product has hit the shelves? We come up with the ideas that make your stupidity suck less!"
How about that? Somehow my guts tell me that BioWare may (or: should) have some job offers after ME:A is released...(just show them what you can do to the ME:3 ending.)
Come on, I didn't say less stupid, but less wrong
We can prove to it that this cycle is different if we manage to broker peace. But if we don't the Catalyst definitely has a point 
Uuuh, I don't know, man, I'm nowhere near them, and also I don't think I could do something like that. I'm just throwing around some ideas and stuff here with other users 