You raise good points. I point out that all villains--and heroes too--are often 'idiots' because the game/story requires them to be, otherwise you wouldn't have a game/story. Take Skyrim for example. If Alduin had waited literally a few more seconds before attacking, the Dragonborn would have lost her head and no one would have been able to stop him. Yet, for reasons that are never explained in the game, Alduin chooses to attack at the WORST POSSIBLE MOMENT in the game, thus setting events in motion to end up getting him killed.
But that is a lame excuse, so I'll attempt to give logical reasons as to why Saren did what he did. Please notice the word 'attempt'.
Vigil suggests that Saren is just the most recent victim of Sovereign. It says that Sovereign has probably been using agents for many centuries, biding its time. This raises the question as to why it had to be Saren to do this. Why not other agents? Vigil suggests it's because Sovereign knew it would get stomped. A Reaper is strong, but if it revealed itself, the galaxy would unite and it would be destroyed before its mission was complete. So it waited. Saren just happened to come along at the right time for Sovereign. The Geth had been made and a faction followed it. It now had its army to launch the attack. It just needed an agent, someone who could move freely without drawing attention. In steps a Spectre who's already known for his extreme actions. Perfect timing.
As for why Saren didn't just charge in at first, I think it's because he didn't know that's what Sovereign wanted. Sovereign was likely hiding its plans from Saren at the beginning because it knew Saren wouldn't play along if it told him up front. Remember, Saren was also studying Sovereign, trying to learn about it. I doubt he immediately went, "Okay, I'll help you wipe us out, or at least prove we can be useful." He was slowly indoctrinated and Sovereign fed him hints and clues to its ultimate plan, pushing him down the path without telling him fully where it will lead. Saren probably didn't know what the Conduit was until Virmire. He probably didn't even realize Sovereign was a Reaper when he attacked Eden Prime. He probably just thought it was a Reaper ship like Shepard at first. Why do this?
Again, it comes down to the fact that Sovereign is just one ship, and it knows it can't stand up to an entire galaxy alone. So it was trying to get all its pieces in place before making its move. It would slowly reveal itself to Saren as he was indoctrinated, so Saren would feel like he was the one coming up with the ideas, not having them fed to him. It was like a game of chess. Position yourself, lure your enemies into the positions you want them in, and then strike.
But Shepard screwed up Sovereign's plan on Virmire. By talking to Sovereign, discovering what Sovereign really was, and causing Saren to doubt himself (at least my Shepard did), Sovereign panicked. It was watching as its careful plan was undone by one human. So, it took the route that you think should have been taken first: direct approach. However, now Saren was outed as a traitor. There was no way he was getting back inside the Citadel alive. So the Conduit, the back door, was needed to get him there and make sure the Citadel was ready to go when Sovereign arrived. Off goes Saren on his mission, using a Mass Relay that puts him right by where he needs to be inside the Citadel. Sovereign itself charges into battle, waiting for Saren to start closing the arms so it won't be destroyed while it works, and then unleashes its true Reaper destructive power. Which, while devastating, was not enough to save it.
So, there are my answers for why Saren did things the way he did. Sovereign knew it wasn't ready, and that it would only get one chance at its task. It waited until everything was nearly perfect, but panicked when it saw all its work coming undone and rushed its plan. The end result is the very reason why it didn't have Saren do things that way from the beginning. Does that help?
