Yet those were his two best films and much better than this.
That's just like... your opinion, man. According to http://www.rottentomatoes.com:
The Prestige: 75%
Sometimes a movie can have a good plot and good fx. I for one thought it was very well done in both areas.
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1. It could never be mandatory, and if it was made so it would be unenforceable
2. If it wasn't mandatory, few if any sites would actually register to avoid being TLD-blocked.
An analogy: "why have marijuana-sniffing dogs in airports since it can be grown in the US?"
This is just a bad design decision just like the FPS puzzles you mention, only there to increase game-play time.