Scanning... you mean like being able to isolate a specific type of metal from orbit?
Blah blah gameplay mechanics blah blah. Equally silly as discussed previously, but we can't really hold something like that against it except for it being boring as fuck.
So EDI, who is partially based on Reaper tech, has scanned examined all the information Cerberus has on Sovereign and the derelict Reaper makes what amounts to a computer 'guess' that the big thing in the room is a Reaper... and this is incredulous why?
"Based on Reaper tech = can identify reapers" is a very vague inference indeed. What's odd is that EDI had some kind of data, maybe RADAR or LADAR or something (only thing I can really think of that it might have, but I have no idea how it got it through unless there's a high resolution radar built into hardsuits or something), and from this giant T-800, concludes that it's a reaper superstructure. That's just kind of really odd, especially since we've only had 2 Reapers to analyze, one of them in a zillion fragmented pieces and the other mostly dead, both of which were shaped nothing like that. If you watch the videos, she makes the Reaper conclusion before he even enters the room itself. How the fuck?
The Energy signature thing is, as we agree, a bit silly. I don't really understand how something being partially made of carbon but also made of things that are not carbon is very useful for identifying things since everything in THE FUTURE (TM) is apparently made out of advanced composites, ablative armor and so on. It's just more stuff the writers didn't really think about. Something to get from point A to point B. Unfortunately, the method they chose doesn't stand up to scrutiny, and point B is fucking stupid anyway with the fucking slushee machine of doom.