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There is an unused model of Dr. Heinz Doofensmirtz found in the game's data, suggesting that he was either intended to be playable or appear as a boss in a scrapped Phineas & Ferb playset.
Contributed by CuriousUserX90
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Buzz Lightyear's Arch Nemesis, Emperor Zurg (who also appeared in Toy Story 2) was originally planned to be included in the game, but according to John Vignocchi, the idea was scrapped because of his status as the Final Boss in the Toy Story in Space Playset.
Contributed by CuriousUserX90