This might have sounded cooler in my head or made more sense but...

This line from Kaiden really struck a chord with me when he says
"We're fighting giant machines from outside the galaxy. Should I be afraid of them or in awe of them? Anything so old, so intelligent.."I think this line really supports IT in a theoretical way not as a "proof". The whole concept of having this Reaper threat in the ME series means that we are facing this very intelligent and indepth nemesis. Hence, the 'simple-not making any sense if literal' ending does not fit the enemy. There has got to be more to it, something more dark, something that demands more from us and a longer battle then space magic.
Every ME game the threat seems to evovle, become bigger and the relation between the Reapers and Shepard/MEU becomes deeper and more complex. I personally believe IT takes this threat and depth of relationship to a new level.
I would very much like to see IT be proven correct and to see the reaper threat evolve as the MEU evovles with the series.
P.S. I have not played Leviathan or other DLC so sorry if I said anything that has proven this wrong.