They're exactly the same, except the original Morrowind comes with a CS CD, which, I believe, is an easier way to access files in the bsa.
I wouldn't bother though, just go for GOTY, it's easier to install, and there's not a bunch of discs to keep track of :shrug:
The GotY edition I have came on 4 CD discs - Morrowind, Tribunal, Bloodmoon, and Construction Set.
More likely the difference is that GotY is already fully patched to v1.6.0.1820, which is required for extenders like MGE. Many mods are created using the expansions and will also rely on Tribunal.esm and Bloodmoon.esm as well as Morrowind.esm - GotY makes sure you have that requirement.