Then way would they built these civilizations in the first place? Their must be something more to all this
Covered, I believe, near the end of the second game, and so...BEGIN SPOILERS
Throughout ME2, humans are being abducted en masse. In the final 'dungeon' of the game, it's revealed that said humans get decomposed into some kind of mineral goo and that this material is being used to construct another Reaper (which, by the way, is one of the stupidest looking final bosses in all of ever).
It's speculated (or stated outright? I'm not sure, it's been a while) that that's the MO of the Reapers: they come back to the galaxy, process all sentient life forms into raw materials, and use the resulting stuff to build Reapers (which, presumably, look more Reaper-y once they're finished). I believe it's also acknowledged that this is incredibly inefficient, and used to reinforce the fact that the Reapers have completely alien, incomprehensible motivations and mindsets.
So... that, presumably, is why they allow civilizations to progress before harvesting them: they need lots of sapient life forms to effectively make new Reapers from. The Protheans were an exception.END SPOILERS
...Of course, there may be more to it than that. I second the position of not wanting to have the origin and motives of the Reapers be fully explained--the Elder Gods analogy was a good one, and part of what makes them so 'scary', if you will, is that they are unknown and unknowable.
As for bringing them into the galaxy en masse...
One way of resolving the story, I suppose, would've been stopping one last Reaper attempt to bring in the fleet, maybe end on the note of "They're still coming, but at least now we have hundreds of years to prepare" or... something of the sort. People might have found that unfulfilling, but that is
what I would have done if I'd been writing the story, and it would've done much better at preserving their mystique as giant, horrid, world-ending space-monsters.
So... I'll just cross my fingers and hope that Bioware doesn't just suddenly de-power the Reapers so they can be wiped out in droves. Story's been epic so far, and I'd like to see it stay that way.