They work so long as Shepard doesn't trust the leads she's getting. Shepard could plausibly be searching those uncharted world's for evidence of Saren.
But I'll agree that urgency can be a problem. I'd simply suggest making the main quest rely less on urgency.
That's basically what I was suggesting for the plot overall.
Perhaps. But even then, Shep should really be checking out a lead she considers unreliable over simply wandering out into the unknown and hoping for the best. If it had been something more like: "these are our best leads [the actual plot missions], but there are some indications of suspicious activity in <systems X, Y and Z> [which turn out to be side quests]" (or someone else telling you the latter part) then a Shep who doesn't really trust the Council to give her good advice might investigate the latter first. But to go somewhere you have no evidence could be connected to your goal over somewhere you have some evidence is is downright stupid.
For some reason I forgot to mention this in my previous post, but I think ME2 did this aspect very well. There were significant periods of time when you didn't have any leads on Collector activity and were free to do as you wished - adding team members, helping out those already on your team, answering requests for aid etc. - but after a certain amount of time had passed (represented in game by doing a certain number of missions, as opposed to any specific mission), something came up that needed to be resolved immediately to advance the overall plot - e.g. a Collector attack - which you had to do then and there.
I think there needs to be some events like this that have a sense of urgency to them, both in terms of story and gameplay. It gives at least the illusion that other people are acting in the world. That it's not just you doing things as you want to. Which, for me at least, really helps with the immersion. Having it like DA:I when things only happen when you want them to makes me feel like I'm not just playing a character but actually controlling the world (take for example, Wicked Eyes.... Despite the fact that the ball is being arranged by the Orlesian nobility, with the Inquistion just being guests, it occurs when the Inquistor feels like going there. No matter how long you spend doing other things, the ball never takes place until you're ready.) Ideally, these missions would be skippable, and you would just have to deal with the consequences of failing to act, but in practice, that's getting into branching sotrylines and bad endings which, as much as I'd love to see that kind of thing, are not the most efficient use of resources from the developers perspective, so the ME2 way of making you do them when they come up is the best compromise.