Alta´r's lengthy rant into the nature of religion seems to be the game lecturing the player about the irrationality of it all and how death ends life forever. This, despite the fact that All Myths Are True and a form of scientific reincarnation exists with genetic memory. It's quite likely that other myths are true in a scientific way as well. It's further undermined by the fact that the destruction of religion is the stated goal of the Templars, the people Alta´r is fighting. Then you remember that Alta´r is in control of the Apple of Knowledge and the thing has a One Ring-like effect on people's minds.
It helps to understand Alta´r may also believe that while All Myths Are True, the nature of the truth invalidates any religious truth from the stories. Likewise, he may just object to the methods of the Templars as opposed to their goals.
It's also possible for Alta´r to have perfectly valid reasons for being an atheist while simultaneously being a dick.
The fact that Ezio never expresses any opinion on the subject of religion and is obviously concerned more with the freedom for people to believe as they will may be Fridge Brilliance by itself.
Expanded universe lore suggests little about the Assassin take on religion by Ezio's time except that religious hypocrisy (aka the corruption of the Italian clergy) is their bigger grievance, best shown when Ezio calls out Rodrigo Borgia on his mocking of Christianity and religious belief despite being the Pope.
Revelations reveals that Alta´r wrote the Codex after Maria died. He might have written that while having a bad day.
This is a fairly easy one. You have to wonder why Ezio and his brother move like champion acrobats and Le Parkour masters even before they've had any assassin training. Then, duh, of course, you remember that they're children of an assassin. Simultaneously, it might be In the Blood as well as their father preparing them in subtle ways for their life ahead.
It's also likely that they learned from friends and through dicking around in Florence. Apparently, if we're to believe the heralds it's become quite popular with the young men to run and jump on top of the roofs in Florence.
It's actually implied/mentioned that Federico had been learning at least some Assassin skills from his father, presumably preparing them for induction into the family business (Federico has to be doing SOMETHING all day, and in his Codex entry it's said he no longer works at the bank after a Noodle Incident). He then passed them on to Ezio and Śin what might be a way to help keep the heat off the Assassins in FlorenceŚ other young men as well.
While reading this, this troper got an additional fridge moment when he realized that in one of the earlier cut-scenes, we see Ezio's dad fully accepting Ezio's trouble with the law / escapades with women. He says it's because it reminds him of himself, but maybe he WANTS him to crawl around the city, fleeing guards.
For me, I wondered how Ezio might be the descendant of Alta´r and how Desmond might have inherited his memories. Then I realized that Desmond doesn't have to be a direct line of descent. As the child of Assassins, it's quite likely that their various families intermarry. Desmond's Ambiguously Brown features help this as well.
There's also the fact that Maria is an Englishwoman and it's entirely possible she returned to Europe via Italy.
It won't make sense by the canon of Revelations for them to be not-related though, since Ezio relived fragments of Alta´r's memory through an Animus-like ancient artifact. It can't be pre-recorded because one device/key is held by Templars for quite some time, but nobody else "see" the contents. Also, the order by which each devices/keys are acquired are random In-Story, but the memories Ezio experience are linear just like how an Animus work.
No, it does make sense. The discs are prerecorded, but likely only accessible by someone with sufficient First Civ genes, which the Templars didn't have, but Ezio does. And you actually do find them in the same order every time, as it's part of the main storyline.
Even before the retcon in Brotherhood, Ezio's shrugging off Rodrigo's gut-stab is foreshadowed by Alta´r doing the same thing early in the first game. And also inflicted by the Big Bad, though you don't know it at the time. Coincidence or Call Back?
In Assassin's Creed 2, I wondered for a bit how the Assassins got a much less buggy and in general better Animus than the one Abstergo had in what seemed like a short amount of time. Also, some of the gameplay changes, such as not having to do as many of the pointless sidequests, didn't seem to make sense from an in-story perspective. Then I realized that Lucy was working on Abstergo's Animus - she intentionally wrote the software badly to delay Abstergo's progress as long as possible.
Yeah, that would be Fridge Brilliance, if it wasn't revealed that Lucy worked for the Templars all along. Being separated from other Assassins, and being surrounded only by Templars, it's quite easy to be corrupted, especcially if you feel alone.
The strongest set of equipment you obtain in Assassin's creed Brotherhood is the armor and dagger of Brutus, which likely you will fight against Cesare with them equipped, think about it for a second.
The reason that no one seems to age over the past twenty years. Remember that we're experiencing things as Ezio remembers them. Most likely Ezio just always remembers them looking the same regardless of age. His sister always looks 15 because in his eyes, she's always been his little sister.
Ezio angrily calls the woman that Duccio is flirting with a whore. At first, I thought this was a bit much... until I noticed that she's wearing an engagement ring.