Among other things, the the complete development of nuclear weapons was shorter
Executive Meddling / Prima Donna Director: George Broussard was infamous in the development team for being a heavy-handed perfectionist. Wanting to keep his beloved Duke as perfect and up-to-date as possible, he went on a decade-long self-appointed quest to apply everything he found interesting into the game, to the point of buying the licenses for entire game engines to force his employees to work around them. Due to this, table flips were constant, and Take-Two Interactive had to resort to threatening lawsuits to get them to speed up, falling through with the threats in 2007, causing 3D Realms to be fired and downsized and the developing rights handed over to Gearbox Software by 2010. It can be said that this made Broussard's reputation end up matching that of John Romero.
Fumihiko Tachiki provides Duke's Japanese voice for the first time ever in the story of the franchise. This is also considered as Hilarious in Hindsight, since his most famous role was voicing Gendo Ikari, and unlike Duke, he wants his girl back, and he'll bring the end of the world along with her!
Limited Special Collector's Ultimate Edition: BEHOLD!◊ The Duke Nukem Forever Balls of Steel Edition! Comes with a bust of Duke himself, an artbook with art through the ages, a limited edition comic book, and other such novelties! All for the heart attack-causingly low price of $99.99! If you live in the US and are near a Gamestop or have access to Amazon, that is. No actual Balls of Steel included, though.
No Export for You: Zig-Zagging Trope: the Russian version of the game is a separate Steam entity. Meaning: it is locked out of Steam's usual language-selection options, as well as any patches and DLC, because the localization company and 2K Games cannot agree on whose responsibility it is to adapt them for the locked-down Russian-only release. All the appropriate access and unlock codes are provided, but they are simply not compatible with the Russian version.
Promoted Fanboy: Randy Pitchford, who worked on Duke Nukem 3D as a junior developer, states he was (and is) Duke Nukem's biggest fan, and made sure that 3D Realms' game wouldn't die.
Talking to Himself: Near the beginning of the game Duke gets into a brief argument with an obnoxious tourist sitting on his throne. The obnoxious tourist is also played by Jon St. John, apparently. It seems the guy has a pretty impressive vocal range.
Start with the fact that the game we got only ever got finished because many of the levels were shortened, merged, or just cut out and work from there.
Many of the characters, weapons and setpieces seen in the early trailers were not used for the final version. An Action GirlDistaff Counterpart of Duke (Bombshell) and a character named "The Prospector" were both absent from the final game (and were likely cut long before Gearbox got their hands on the game).
Ben "Yahtzee" Croshaw of Zero Punctuation was asked to write the script at one point. Most of the development team absolutely loved his outcast, but George Broussard was more skeptical and kept asking "Would Duke really do/say this?", and eventually it was turned down. According to Yahtzee it portrayed Duke as an ironic character and made fun of everyone around him, as he believed it would be the best way to reintroduce Duke Nukem to a modern audience. It got scrapped in favor of "Duke played straight in a silly world" that we see now. Yahtzee was given a chance to revise the script to go with this tone, but he declined because that didn't make any sense to him.