To be fair, I believe it's heavily understated the exact timeline of Destiny. The Iron Lords existed before the Tower, Saladin isn't exactly a regular fixture - The lore right up until Rise of Iron painted them as semi mythical figures, the same way the former Vanguard members like Osiris and Saint-14 were.
Someone did. Saladin. Who kept watch over it and (presumably) killed anyone who was close to uncovering the truth/releasing SIVA that he didn't trust. An Immortal Guardian who taught Zavala AND Shaxx (ergo the two Titan Mentors), who wants something kept hidden? I'll tell you right now, he's not sitting around during the three weeks he's not in the tower. Destiny's timeline isn't measured in decades, it's centuries. One has to be cognizant of the fact that Saladin is, at bare minimum, four to five hundred years old.
Also, if you read the description for Glimmer, evil Nano-tech totally had a buildup/was implied. Just in the background. Glimmer is basically non-evil SIVA.
Believe me Ace, no one has more criticisms of Destiny's story than me, I just happen to also be the Loremaster of all the groups I game with There's a LOT of stuff hidden away and inferred if you just take the time to sit down and think about it, it's one of the few things I truly love about Destiny.
Examples being Dredgen Yor and Shin Malphur, The Book of Sorrows, Osiris' and Saint-14 and the Vault of Glass etc etc etc. I won't Deny Rise of Iron's story wasn't exactly strong by any means, but for a DLC expansion to a MMO shooter with a history of exceptionally terrible story content? It wasn't as bad as everyone would have you believe.