It doesn't ruin it. Because Shep thwarted their plans, they may have given up on a human-shaped Reaper.
ME2's paper-thin plot, why don't you make sense? Off to wiki I go.
Okay:
:|
		
		
	 
True, but it ruined it in the sense that when I first thought of it, it was in the context that the Reapers were still just a super advanced synthetic race that harvested advanced organic species for their own benefit/reproduction and not as some crumby galaxy janitors that were "saving" organics from annihilation by their future synthetic creations. 
There is something inherently interesting about an enemy being virtually unknowable, because it is in fact relatively foreign to human history and experience, especially in modern times. We have never faced an enemy that operated on the sole desire to destroy us completely and without mercy for no other reason than to do so, we've always been able to understand, to some degree, the actions of others and operate on the ability to negotiate with them at some point during a conflict even if its to surrender and submit to conquest, we'd still survive. This wasnt possible with the Reapers, it really was a situation where you fight or you die, as corny as that sounds.
Despite all their differences the various races of the galaxy could still understand each other if they tried, however limited that understanding was, and arrive on some common ground and work with one another in shared interest to fight together and resist the Reaper threat.
I mean thats a major theme in the game, being able to communicate with others to avoid hostilities and settle disputes. Whether its getting Chairman Burns to help victims of L2 implants in ME, to convincing Saren and TIM, appealing to whatever humanity remained in them, that they were wrong and were being controlled by the Reapers, to interacting with Legion and learning more about the Geth, realizing they didnt want to fight and using this new found information to help end the centuries long hostilities between the Quarians and the Geth. These and a whole host of other events small and large were often times affected by the choices you made in conversations and not just your actions in combat.
This is another reason the Catalyst ending was so terrible, there was no conversation and back and forth on the issues, we're told a bunch of stuff completely out of left field and without any discussion are forced to make a dramatic decision we barely understand the ramification of, let alone the rational behind.