I can definitely agree that the series can be split up into smaller trilogies or thematic trilogies as you put it, but without digging into Patrice's brain—I am fairly certain he was going for something between a psychological "mindfuck" piece of fiction mixed with a historical thriller.
Then the feedback from Assassin's Creed came in and Patrice kinda split the difference between the modern day thriller plot, and the Renaissance storyline with a more typical open world game design. The action focus in AC2 is prevalent as opposed to the ancient-espionage vision that AC1 had. Those changes were especially noticeable in a post-Arkham world, so they needed to up the pace and smooth out the combat.
All this to say, I think the "vision" of the series was one thing (thriller, mindfuck, espionage, stealth), but Ubisoft and Patrice switched gears really quickly into something that works better as an open world video game.
So I guess the question on Game Thrasher was: Has Assassins Creed Betrayed its Roots?
I guess I am arguing Ubisoft abandoned it's roots waaaaaaay before AC Origins. I don't think they "betrayed" it, but by having all of these smaller trilogies they definitely don't make this series trademarks easily identifiable other than climbing towers and haystacks.