But the fact is that the Catalyst and his motives were foreshadowed, you just don't like how its done, but facts are facts.
Oh and when does Shepard tell Joker to leave them on Ilos? He doesn't. There is no info given in the game that he was supposed to leave and rally the fifth fleet. Simply put, the writers forgot what they were doing and created a plot hole which casues a Deus Ex Machina. And the n people were complaining about Joker abandoning Shepard in ME3, wow hypocrites.
Nevermind you cannot prove the plot whole you claim ME3 has. How does Soverigns motives contradict the Catalyst from ME3? There is NO PROOF as Vigil's info may in fact be limited (as ME3 proves that Prothean VI's knowledge are limited with the fact that Vendetta was wrong about the true nature of the Catalyst). I can easily play your game. The Protheans sabotoged the Keepers, which allows Catalyst to open the Citadel relay. This leads to Sovereign to attempt to find a way to manually activate the relay. Basically the Protheans paralyzed the Catalyst's functions. But I can play this much easier...how. Because the Catalyst states that the Crucible is part of him, that means the Keepers.
Mhm.. whaaat?
Shepard can communicated with Joker beyond the radius of a relay. There are communication channels that work throughout the whole galaxy, that's how he orders the Human fleet attack from beyond the relay. Considering all the Geth ships that were on Ilos went to attack the Citadel, I think the whole thing is pretty reasonable if not very well explained. Then again there's a similar convenience in ME2 but it in neither game does it ruin the lore. Feels forced? Yes. Game altering? hardly...
Catalyst was clearly told us to be the Citadel. I don't invent stuff, your precious VI on Thessia tells it plainly to our face. How does he know that it's the Citadel? How does he know there's someone behind it all? Oh wait, he uses the same knowledge as Vigil basically mirroring his function in ME1. That's actually a clever circle which would work if he was right.
Then you claim that he was wrong about Citadel being the key but his by-bare-threads foreshadowing of an AI is irrefutable and clear and timely... ye, that's sound logic.
So the AI who is the collective consciousness of all the reapers lives on the Citadel yet the reapers leave one of their own every cycle to watch and activate the new cycle? Can't the AI do that himself? He engineered the whole thing, didn't he? The whole keepers got overridden thing is also a farce now because why would he allow that to happen? The guy has Reaper control/destroy and galaxy altering switches that function with an extra battery, but he doesn't do anything to enforce the cycles he's so hellbent on perpetuating? Why is Sovereign even left behind?
That's what happens when you introduce the new lame character in the end and you don't know what to do with him. And while they rectified his reasons with EC, they didn't rectify the whole reason for him being there. You know... because that would cost too much for a free DLC.