Now that GOG released X-wing, I have been torn which version to play. I played the original avidly back in the day, but not the newer one. I like the mappable joystick controls of the newer 1998 version, and it controls nice and smooth on my flight stick. I like the nostalgia of the original (new newer one seems dark and empty), and I can hang with the polygon graphics and 320x240 resolution. I find just having two joystick button passable, but the deadzone seems jumpy and erratic.

I am also worried about mission structure in the newer one. I hear that the newer one is made to be easier, but one of the things I like about the old one is the difficulty. The reason space shooters disappeared is because they became simplified to the point that it is nothing more than flying in circles and shooting, but one of the things that made X-Wing and Tie Fighter great in their day is that their difficulty required you to play strategically, configuring your systems, sending wing man orders, and picking your flight path at the right time to meet mission objectives. If the missions became easier that would break the need for this strategic play.

Also I have been trying to track down reviews of the 1998 version when it came out. I figure most of the differences and gripes would have been covered in that. If anyone knows of a link please add it. Thanks.

I've only played TIE Fighter so I can't give deep insight but I imagine the biggest difference is it doesn't have the imuse midi music. Buying it on GOG gets you both versions though so you might as well just try them out.

Edit: I found this (again about TIE fighter but still, a lot of overlap I believe)

http://www.gog.com/forum/star_wars_tie_fighter_special_edition/the_differences_between_the_1994_and_1998_versions