I think that I enjoyed Fate of Atlantis more, especially because it had the three paths to give it some more ways to play. I avoided the "Fists" path because my keyboard didn't have a number pad.
I went back to both of them, decades years later, and found Last Crusade to be much more challenging in a way that games no longer offer (besides Dark Souls) -- they let you make mistakes which hinder or make completion almost impossible. You could get pretty far in to Last Crusade and not have the required items to progress further.
Many gamers hated this kind of "getting irreversibly stuck" situation of early adventure games, and in fact Lucasarts made a conscious effort to avoid it in later games (e.g. Full Throttle, Monkey Island, etc). You couldn't even die (yes, I know about the dying easter egg in Monkey Island).
This was in contrast with Sierra Online's adventures, which had plenty of surprise deaths and deadend situations. This led to saving frantically at every step, which isn't particularly fun.
I loved Sierra games -- the first three EGA Space Quest games are my favorites -- but I see the point of avoiding player frustration.
I don't like getting stuck permanently. Even in Dark Souls there are no ways to get irreversibly stuck, although you can make it significantly more challenging by killing certain NPCs along the way and losing the ability to use the services that they once offered.
