Forum:Is it just me or has ME1 stopped to make sense given the ME3 outcome?

Correct me if I'm wrong, but the whole plot of ME1 has now stopped making sense after we know what happens in ME3. To be honest ME1 already made less sense after ME2, but I could live with that. Let me explain what I mean:

In ME1 we learn that Sovereign was left behind to tell his fellow Reapers to come out of dark space to annihilate everyone once they reach a certain level of evolution. But to do that he needed the Citadel to send this signal.

Question 1) Why does Sovereign need the Citadel? Answer: How do the Reapers get to the Milky Way? The use the Mass Relays. Why can't Sovereign just use the Mass Relays himself to get back and tell his fellow Reapers? But let's just say he was too lazy and wanted to call them instead. Question 2) If the Catalyst controls all Reapers, as it says, why all the fuss with Saren and Sovereign? Answer: Either just tell Sovereign to tell the other Reapers, or, since ALL Reapers are controlled by the Catalyst, just tell them to come back. But let's just say the Protheans really found a way to outsmart the Catalyst and disable any signals to the Reapers...

Question 3) Since both Sovereign and Catalyst failed and were not able to send a signal to the other Reapers, how did they know it was time to come back? Answer: They found out through the Collectors, since they had control over them for the last 50000 years, in which case what's the point of Sovereign being there. But let's just say they didn't use the Collectors for this and just come back exactly every 50,000 years anyway... (in which case ME1 makes even less sense)

Question 4) If the Catalyst apparently lives on the Citadel already, why the need for Sovereign or Saren to take control of the Citadel? Answer: There is no need for either of them. The Catalyst seems to be able to indoctrinate people by itself, so why not just indoctrinate the whole Citadel? Or even if it can't do that, why not just kill everyone on the Citadel by for example venting the whole atmosphere? The Catalyst obviously lived on the Citadel for thousands or millions of years, it must have control over it.

Thoughts???