The game has limitations, and things like auto vertical shot trajectory were implemented to address them and make it playable. It's the same reason the level designers were making bridges out of sprites instead of geometry. One of the key features of Ken Silverman's build engine was the ability to have elevated sectors. Not being able to place enemies in any area where sectors of extreme differing elevation were present because the player then would be unable to shoot up at or down onto said enemies would have severely lessened the usefulness of this feature. Thus, the shot height auto correct. In regards to disabling this feature so that you have to "work for it" and "rely on playing skill", I would have to disagree. I would argue that by simply adopting the modern FPS control scheme, you are in fact making the game much easier for yourself. MUCH. Think I'm wrong? Load up a modern FPS, bind your keys the traditional way with arrows for movement, ctrl for fire and alt for momentary strafe toggling and join an online multiplayer match of said game. Or don't even do that. Play the solo campaign. You know what would happen, and so do I. With DN3D, circle strafing with the mouse and keyboard alone are enough to break this game, whos AI is tested and tweaked to be of moderate difficulty when you cannot do this fluidly. Circle strafing in days gone by was considered an advanced tactic because you constantly had to release and depress the alt key to trigger or cancel the strafe and instead, turn. This caused circle strafing to be more of a series of steps rather than the smooth arc generated by simply moving the mouse to the side while strafing. But, I digress. I'm sure everyone knew that already. Now if you were to say, argue that you simply preferred the modern FPS control scheme, have decided to play the game that way, and have therefore nullified the need for this shot height correct... I'd say that's fine, and that you're probably right. I'd tell you to go for it. But you won't be "working for" anything and will be diminishing the skill the game requires of you. You could say that you're okay with that, and if you are, I am. Perhaps you would opt to turn up the difficulty to compensate for the new control scheme. Perhaps I'm making your argument for you. Regardless, you're a grown up and can make those kinds of decisions for yourself.
For all those reading this thread attempting to find ways to enable mouselook in Duke Nukem 3D, whatever your reason, eduke3d may not be your only avenue and it may be possible in the game natively. Now of course, page up and down buttons are default mapped to be a rudimentary "look up and down", but it is hardly usable and not a true look up/down, but rather a strange perspective shift. Vertigo sufferers beware. However, if I recall correctly (away for work and cannot access my computer and subsequently, my copy of DN3D), you can enter setup (a completely separate executable, setup.exe) and invert your mouse (DN3D's default is inverted, so you have to invert the invert, so to speak), then while still in setup rebind your keys to your preferred WASD configuration. Exit setup and load the game itself. While in game, press U to enable mouselook aiming. This may serve as a way to closely emulate modern FPS control scheme, if one so desires, therefore not requiring eduke32 for this specific outcome. But, my memory is not what it once was, so someone may need to confirm that this is in fact possible, or adjust the required steps.
EDIT
*highfives Mabrookes. still flexing*
Post edited September 24, 2015 by DarknessConcept