It's mainly just more colours and Red Book Audio music, rather than the cheap sequenced MIDI of the Megadrive/SNES versions of EWJ2. This version is also available for PlayStation and PC, so it's not particularly "a Sega Saturn game worth owning", as it were. I recently got Duke Nukem 3D on Xbox Live Arcade, and while it looks great (in a retro kind of way) in 720p and at 60fps, it's still visually missing something that the Saturn version has. The SlaveDriver engine of the Saturn version gives the game a certain 'zing' in the way it moves.
Plus, looking up or down in these 2.5D games (Doom, Duke 3D, Hexen, etc etc..) sucks balls because everything distorts. The engines these games run on are actually 2D engines. They are just rendered in certain ways the give the illusion of moving around in 3D space. Specifically, certain vectors are given height values, and thus create 'walls' around the player. It really is only a step up from the rotating pixel 'Mode 7' of the SNES (used in Mario Kart, etc).
In these games, vertical lines can only be rendered as absolutely straight vertical (north-to-south if you like) lines. The illusion is very effective when looking at a 90 degree angle, but look up or down and things quickly distort in a very strange way. At the time, Duke was seen as very advanced, as it really pushed the '3D' envelope more than Doom etc had before it, since it had a more convincing simulation of 3D space in a 2D engine. Probably the most convincing.
Duke, unlike Doom, could handle rooms on top of rooms (Doom and all the games using the Doom engine could not), so long as both spaces were not visible at the same time. This is why the water in Duke is not transparent- the game has to treat the 'above water' and 'below water' sections of any given room as two separate rooms. Diving into the water causes the player to be warped to the other 'room', which is made to look like the underwater portion of the room you were just in.
I have no idea why I just wrote all that. Anyway, Saturn Duke is the tits, even if the controls are really crap and the frame rate is quite slow compared to the original version running on modern hardware. Playing Duke online on XBL really rocks, though. I've been playing it a lot. It's a right giggle in co-op.