Pretty much.
Why does sovereign talk to shepard at all instead of just firing at the base from orbit, since its obviously compromised? Why was it important to find the conduit when its entire purpose was just to let saren walk into the citadel and get to the door controls? Why did benezia keep the rachni queen alive once the information was extracted, when a single push of a button was all that was needed to kill it? Why wasn't feros nuked from orbit by the geth? And other such questions of plot.
Why did Benezia keep the queen alive? "Her children were to be ours." It was planned that the Rachni were to be bred and used as a Reaper weapon. But then Shepard showed up and ruined it all. So if Shepard died, it would be okay, but she knew she was going to die and that Shepard would either kill the queen or free it and the Reapers would get nothing.
Why does Sovereign talk to Shepard? Because of reasons. It is to demonstrate the evilness of the main antagonist. See Saren was merely the obstruction.
Why doesn't Saren enjoy a latte and walk into the Citadel door controls? Well, how many geth could he get through the conduit before Shepard? He walked on foot, and it was quite a walk. Shepard drove usually running over geth -- who really stopped to take out the geth?
And never mind that the lore went out the window -- shouldn't everyone have bounced off the Citadel let alone splattered on the top of the cavern? Hence that makes the relays more like jump gates.
Why wasn't Feros nuked? Because of the Treaty of Farixen. It banned nukes even though the Geth didn't sign it, their masters probably did.
Why didn't Sovereign blast Virmire? Because Shepard needed to do that.
Why did Shepard have to put out the refinery fire? What did any Shepard know about putting out refinery fires except for maybe the Engineer Shepard? Yes I know that the game walks you through it, but seriously.
Why does Shepard have to decide the fate of the Krogan?
Why does Shepard have to decide who lives or dies between the Quarians and Geth? "I don't like Gerrel, therefore all you Quarians die!" "Sorry Legion, no reaper code for you." OR "Peace for all, then I'll destroy you geth at the end."
Why do Shepard and Liara stand there doing absolutely nothing while Ashley gets the snot beat out of her?
Why do Shepard and his/her team stand there doing nothing while Kai Lame hands Thane his ass?
Why doesn't Shepard bust a cap in Kai Lame's ass on Thessia at point blank range instead of talking to The Illusive Man?