I always wonder why ZDoom even has that "monsters see invisible players" compatibility option at all. SNES Doom is about the only version of Doom I know where monsters can't see you when you're invisible. Is it for Hexen/Strife compatibility or something? I admit that I never play those games.
The most significant, irreversible changes when comparing ZDoom with vanilla is that ZDoom made arch-viles invulnerable to their own attacks (they used to be able to damage themselves if they were too close to their targets when they blew them up), and lost souls now focus on their targets, whereas vanilla lost souls would strike only once at monsters that struck them, then would forget and return to attacking the player. Having compatibility options for these features would be nice, especially with the lost souls, since that was a unique, special trait of theirs.
And I doubt it can really be helped without rewriting the movement code, but it always seemed like arch-vile jumps gave you a lot more air in ZDoom than in vanilla, potentially letting you reach ledges you wouldn't have been able to in the classic engine.
Another minor yet obnoxious bit of ZDoom behavior for vanilla enthusiasts: DoomGuy's face. If you hold the fire button down long enough, DoomGuy will start gritting his teeth as he unleashes a torrent of bullets. However, his facial expression seems to be tied to the actual button press in ZDoom, where in vanilla, it seems to be tied to the animation frames of the weapon instead. Why does this matter? Because holding down the fire button for rapid fire reduces the accuracy of your shots. In vanilla, if you saw DoomGuy gritting his teeth, you know your accuracy is reduced, and you have to let go of the trigger for it to reset itself. Once DoomGuy's face is back to normal, the next shot will be accurate. But in ZDoom, if you let go of the fire button at any time, even in the middle of a weapon animation, DoomGuy will go back to his normal expression, even if he's actually still in the middle of a reduced-accuracy, rapid-fire rampage. A really tiny detail, but it still throws me off sometimes.
But again, those are really tiny things. Overall, ZDoom has gone a long way to give the player the opportunity to play Doom as it once was. There may still be some rarely-used vanilla tricks that don't quite operate properly in ZDoom. (Didn't some Memento Mori map require a spechits overflow? Not sure ZDoom could emulate that.) But in the end, I imagine most vanilla maps will work fine and play as the designers intended.
Now we just need to have people stop making "vanilla" maps while only using ZDoom to playtest them....
And, of course, if you really want brutal authenticity with your Doom experience, that's what DOSBox and Chocolate Doom are for. :)