Why not have something what SW did with redux and classic?
It's not a lot of extra space to drop in eduke stuff alongside a DOS release
If someone wants to switch between "1996" and "2014" modes then they can always do it.
Playing the game with 1996 intro demo files / multi player and old bugs like they remembered it.
If they want cool stuff that people have been cooking up for many years then they can kick eduke open.
I would go for eduke myself as there are so many cool mods out there that people should be able to play with little to no effort.
Considering the crazy amount of improvements done to Duke over the years, I'd say that eduke is still very faithful and doesn't add silly things like a sound when finding a secret in doom ports.
Not to mention that if they want to do their own maps, Mapster32 really kicks stock build's ass.
I consider content creation a really major aspect as well, no other port really enhances that side.
eduke also allows much less obscure formats to be used with a mod.
As much as I love megaton's multiplayer support and it feels like a nice compromise, it's seems a dead end when it comes to modding/support and from what I have gathered the content seems to be done with mapster32 anyway.
Also eduke has linux / osx support to some degree from what I remember.
Anyway, that is my angle on things, from a bit of a modding perspective.