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I emphasize Mallory Square for sunset, and possibly a sunset cruise. See the Truman White House, and Key West Lighthouse, too. The Key Deer (near Big Pine Key) are fun to observe and photograph. Bahia Honda has pretty beach & water, Seven Mile Bridge a marvel. The coral reef is good for snorkelers, not so sure about the glass bottom boat.
As suggested, time in the Everglades is very rewarding, both wildlife and landscapes. The road to Flamingo has several good spots, the best being Anhinga Trail. The Shark Valley section is also good.