1.) Remember the Mu Relay? That got hit by a super nova. It survived. We can't just blow up relays whenever we feel like it. Besides, Cerberus wanted to acquire Collector technology.
2.) Many people have wondered why the Reapers constantly allow civilizations to build itself up, only to swiftly destroy it. There are many theories as to why. You could think that the Reapers are just using organics as a food source, but arguably there are easier ways to cultivate and sustain organic food than allowing civilizations to constantly evolve and then fall. Rather I think they do it because the Reaper's culture involves preserving the most advanced and valuable species for eternity as Reapers. Reapers are not one single species, but rather a combination of all species ascended into a higher form of life. The best the galaxy has ever produced, all united under one banner.
The Reapers were not just trying to build any ordinary Reaper. They wanted to build a Human Reaper. Not to lead a massive attack against the Citadel, but rather becuase this is the Reaper's culture. They believe Humans are the species with the greatest potential. If they were just trying to build a generic Reaper, they could have used any species. Arguably it would be a lot easier to target something other than human colonies. But they specifically wanted to turn humans into the Reapers. Think about Harbinger's dialogue. He refers to the process of turning humans into genetic paste to fuel the larva's growth as "ascension". Why use that word in particular? Why not call it "assimilation"? Or "consumption"? "Ascension" implies that they are raising humans to be what they consider to be a higher form of life. They see value in humans.
But what about Sovereign? He didn't seem to like organics at all. Why turn them into Reapers. Well I believe that the Reapers may have considered the current organic "crop" to be a failure, not worthy of being turned into Reapers. This could be for a number of reasons. I think it's because the galaxy had a very diverse category of sentient lifeforms, with no one species appearing to be dominant. The Protheans appeared to be the undisputed rulers of the galaxy at the time of their downfall. This is the Reapers idea of the perfect organic race to harvest. One species that follows their predetermined line of technological advancement, rather than a handful of species that all do so at the same time. So the Reapers were all set to just wipe every race out and start from scratch. What changed this? Well humans killed a Reaper. The game often alludes to the idea that by killing a Reaper, we grabbed their attention. To delay the extinction cycle and kill a powerful Reaper in the process would probably interest them. So Harbinger now thinks that humans are worthy of ascension into the ultimate life form.
If you're wondering why they didn't do this to the Protheans, it's because the Prothean Reaper failed. Instead they turned them into the Collectors, so that they would still serve a purpose.
In short; Reapers wanted to create a Human Reaper for cultural reasons, not military strength.
And I don't think this Reaper was a backup plan for Sovereign. It was still far from completion when you encountered it, and apparently the Collectors have been harvesting since before Sovereign died. Harbinger has some other way of reaching the galaxy. I don't think the human Reaper would have attacked the Citadel.
3.) Remember that datapad at the end? The ony with all the data on Harbinger on it? Yeah, I'm pretty sure that was important. And we stopped another Reaper plan. I don;t see what the problem is.
If you really want a plot hole, ask yourself this; why did they all get on the shuttle during the IFF incident?