That was BW throwing the lore out of the window and making ME2 plot even more pointless than already was.
I wouldn't say that.
There were a lot of Protheans harvested, and to think they all existed at only one base is equally silly. To also assume that Mordin is 100% accurate about anything and everything in the universe is also foolish, for I do believe he admits when he's 'made a mistake' especially when the big picture is made of many little pictures. The Leviathans could bring down a Reaper just by thinking about it; breaking the bond between a group of Collectors from the Reapers would be less difficult. Many of these Awakened died in the process, but there were those that survived. It's possible that the Awakened are really just 'husks' for the Leviathans instead of the Collectors, however.
What bugs me about the Collectors is that the Awakened ones we get to play as in the Multiplayer must have been long-serving specimens if they must think themselves to be Protheans. Most of the Collectors are described as cybernetic-enhanced clones, so the Awakened must be from the original stock. I'd have preferred if these Awakened were not of these original few, as I think seeing more about how these 'nothings' adapt and become 'something' would be interesting. . .that and I think the Collectors and their aesthetics are cooler than the Psuedo-Space Samurai look of Javik and the Protheans.
The other thing that bugs me is that the Reapers do not deploy or do not have any husks from other species of the Prothean Empire or from cycles beyond. It could be possible that they only used the 'original' Prothean species for the collectors due to their quad-based DNA and thus the others were simpler to just 'Reaperize' in Destroyers and Capital Ships, or the other husks were used but excessive cloning and maintaining over the course of two or more cycles would be a needless expenditure. Allowing the Collectors to operate semi-autonomously and as a second set of eyes in the Milky Way besides a slumbering 'vanguard' (Harbinger) saves them the effort of keeping their husks alive and could explain why they can only field the Collectors and any race they are harvesting in the current cycle.