I'm still upset at how little screen time the Architect got in that game. The Calling made him a very interesting character, and he just shows up 2 or 3 times in the game. Argh!
I actually prefer it when that happens.
We saw the same thing with Saren in Mass Effect who appears in brief cutscenes throughout the game, but only directly encounters Shepard face-to-face twice, once on Virmire and during the final fight at the Citadel. Same with Loghain in Origins, who spends the entire game consigned to cutscenes and who the Warden only encounters three times (Ostagar, at Denerim with Eamon and during the Landsmeet) during the entire game, unless you decide to recruit him.
Keeping characters like Loghain, Saren and the Architect apart from the protagonist and limiting them to short, important scenes prevents them from being over-exposed, making them seem larger-than-life and more memorable to the audience.
(And to use another example of the same thing, Darth Vader is one of the most memorable things about Star Wars: A New Hope, but he's only in a handful of scenes and very few of them are with protagonists. He's in at least three scenes with Leia, one with Obi-Wan and he never even interacts with Luke Skywalker and Han Solo at all except during the space-battle to try and take down the Death Star)