This reply to that will be a spoiler to everyone who hasn't bought the DLC, so I'll use the spoiler tags, but it is directly towards the reapers and the citadel:
If you ask Javik a bit you'll get to know that he's never seen the citadel because IN THEIR CYCLE THE REAPERS TOOK CONTROL OF IT. And that was long before he was born, so it's safe to assume that the citadel hasn't moved much (if at all) from the time the reapers last controlled it.
Well yeah, looks like a great idea... well, the destroy-ending kinda fucks them over, like "here, we'll help you kill us!"...
And the control ending... well, still not entirely sure who takes control of what and how that works... but also ends the cycle and thereby defeats their reason of existence.
Same goes for the Synthesis-ending, defeats the purpose of the reapers, at least what we were told by the god child. If you mix organics and synthetics... well... how exactly does that solve anything? Wouldn't they still have to continue the cycle until only pure synthetics were left, because otherwise the "mix" could build new synthetics that would, according to god child-thinking, definitely kill their creators.
So all three endings go directly against reaper-philosophy... so one can pretty much say that the reapers shouldn't have wanted to give their enemy such a huge advantage...
Oh and the catalyst IS the citadel, it wasn't made the catalyst by the reapers, it was implemented into the crucible-strategy by whatever race that thought of it. They probably thought something like "well, the citadel can do some kind of crazy stuff, could we use that to kill the reapers?" and found the answer to be "yes".
That may very well be possible... they would've had to adapt to the changes made with the catalyst-plans, because it wasn't there from the beginning... but yeah, that might be possible, all speculation though. AI isn't really known for changing it's mind out of whim, but maybe the reapers are different, who knows >_>