lets be completely truthful here:
if Duke Nukem Forever came out in either 1999, 2001, and or 2003. It would been mercilessly called a Half-Life 1 and 2, and Doom 3 clone and trust me, being called a clone in the early days would have killed your game dead back in those times, especially being called clones of one of the popularly rising games like Half-Life and seasoned vets like Doom. Whether or not you liked the DNF we got; there is no denying that calling things a [insert popular game of that genre here] clone would fuck you up, i mean, look at Saints Row; people for years called it a GTA clone, now they added aliens and shit to deviate from that moniker, but alienating their core fanbase (I.E. the people that liked the 1st 2 Saints Row games) in the process, all because it couldn't get away from the stigma of a clone
their best bet was to release the 1997-1998 build to not deal with the stigma of a "clone of popular game" and the immeasurable hype let down, that way if it was considered a bad game (which I doubt, but lets be hypothetical here) it would have been dealt a swift death and ignored pretty fast
also: "they changed Duke way too much, he's a douche now" you realize he was a douche back in DN3D, that was his schtick, be a 80's action hero, that if you met in real life; you'd assume he was a douche too, that spouts one liners and saves chicks from aliens