Most of the changes are too numerous to list. Physics, rendering, input, RNG... almost all of it has changed in some way. Some might be noticeable, but lots of it isn't readily apparent.
Taking RNG for an example. Doom and GZDoom are both
deterministic, meaning that given the same "seed" (starting conditions) and actions, a game of Doom will play out exactly identical every time, because the exact same random numbers are generated. This is how demos work. But since the RNG engine in GZDoom has changed, it outputs different random numbers than the RNG in classic Doom. Superficially this won't be immediately apparent because the main source of "randomness" between games is the player's actions (since players aren't frame-perfect machines). Monsters will appear to move in similar patterns in GZDoom, but some players might notice the SSG feels
very very slightly more powerful, since due to problems in Doom's original RNG the maximum damage per pellet is never rolled.
Most non-visual changes are like that. Very subtle, hard to notice unless you know what you're looking for or make a direct 1-1 comparison, but might contribute to very slight almost imperceptible differences in game-feel.
