Why does anyone give a shit about the site? Just read the -blam!-ing article already, who cares?
It's a really interesting article, and a great analysis of both level design in general, and the design direction of Halo. A lot of fascinating little points.
That said, The Silent Cartographer doesn't quite have everything that makes Halo brilliant, as it lacks the enemy vs. enemy encounters that made the last three levels even more fantastic (although not [i]as[/i] fantastic as Assault on the Control Room, IMO, but that level's physical design is unmatched in Halo's history).
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I would agree that TSC was the most iconic level, and a fun one at that, but I don't know how Kotaku made the iconic=best connection. I think tropical environments get an unfair positive bias in games simply from the "wow factor". Like you said though, I agree that AotCR was a better level in terms of combat engagement and diversity. That's honestly where I had most of my Halo CE campaign fun, partly due to the sheer size of the level.