Yeah, it's kinda sad that nobody found the Klendagon Cannon, because it certainly would've made an interesting alternative to the Crucible. Other favorites include Tali's face in a non-cop-out fashion, Haestrom's sun (we even visit the damn thing, but only to politick around) and the resolution to flirting with Parasini-san and Shiala. I am yet to see any mention of them at all, other than there's an expy of Parasini you get to work with on the Citadel, but no subtext =(
I expected a closure for the prothean vision you unlock with the Consort´s pressent. It was supposedly a flag carried from ME1 that never got developed.
Javik talks about how Prothean tech works, explaining the mechanics behind this device, plus he does get into detail about how the Protheans studied all the races that we know when they were still primitives if you pester him and bring him along to homeworld missions. There's a VERY VERY GOOD reason why people hate "From Ashes" being paid DLC, and boy am I glad I have the CE.