Uru does indeed have the notion of collecting. Isn't that what journey cloths were?
Like Lontahv, I would suggest that it does not have to be the collecting of physical objects.
On the other hand, Cyan itself didn't hesitate to break the mold in Uru. They have stepped beyond Myst-like puzzles.
Why then souldn't you break the Uru mold and create entirely new kinds of puzzles and mechanisms?
An interesting example is the game "Mysterious Island", currently available on GameTap.
It lets you pick items up, and then combine them to form new objects that you will need to progress.