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All of your arguments are related to race against time, must catch Saren as he is threatening the entire galaxy. Trumping up some sense of urgency is a time-honored technique to raise drama in a lot of forms of fiction, and its especially true of games.
How many times have you gone to do some omg-hurry-hurry-oh-so-urgent mission yet had plenty of time along the way to harvest elfroot, search for thermal clips, hack loot crates, or stop and chat w/ NPCs? Or work in a few other missions first? A lot, I'd wager. Except for those rare occasions when something actually *is* on a timer, I've become pretty much impervious to the notion that any of it is particularly urgent. Of course, as players, we also know that we can turn off our rigs at any moment, come back a year later, and the game world will not have changed.
But we're not Shepard, and Shepard might believe that catching Saren must be priority 1.
I admit that I'm willing to erase those 3 leads from the journal, and play the game as if Shepard has no leads if that's what I need to do to fully explore and enjoy all of the content the game offers. I personally feel that it'd make for a much better game if Shepard was not given those leads when s/he was.
And I don't think it's especially unusual for individuals to "erase" parts of media that don't really work for them. I think there are quite a few places in the trilogy (and other media, too) where people need to handwave something or other to enjoy the work.
But I play these games for the RP, not to be told a story. When I want to be told a good story, I look to literature or film, not videogames. I think that's a key difference - some people seem to favor having the devs manage the availability of content for story pacing reasons. I'm not really in it for their story, so for me, that's just gating content I'd rather have available sooner.