Just finished replaying Last Crusade and Fate of Atlantis ahead of Dial of Destiny's release. Been 5-10 years since I've last played them, and still enjoyed them both for different reasons.
Crusade is definitely the rougher and more dated of the two in terms of interface and visuals, and even tonally it's a little all over the place as well, but in terms of having an open-ended nature, it's remarkable how many variations of puzzle solutions there are, some of which involve entire sections being able to be bypassed while other sections are made more fun with the optional alternatives. It makes the game more re-playable than it might have been to know that there are multiple ways to play it that can potentially change the game significantly. I will be honest and say that given the number of easily findable dead-ends, I found the game very difficult to play without a guide. Thankfully, Thunderpeel's Game Guide is still proving useful after all these years! Music in the game is fairly limited as in most of the older games (and mostly lifted from the movie) but it's still nice to hear in MIDI form regardless. Overall, a good game despite the technological limitations from the time. (Also, Last Crusade is easily my favourite of the Indy movies so I'm happy to have the game available as a companion piece.)
Fate of Atlantis in my opinion still holds up as easily one of the best of the LucasArts Adventures. Primarily, again, because of the replayability, most of which is due to the three paths, and all three are worth replaying the game for to experience them all. That being said, I don't find the names of the paths (wits, fists, team) to be completely representative of the puzzles themselves (i.e. I didn't find the wits path significantly harder than the other two, Sophia reunites with you in the other paths eventually, and in the fists path there are at least two fights which are far more preferable to skip!) But yes, the three paths is a definite standout of the game that sets it apart from a lot of the other LucasArts games.
The soundtrack despite being MIDI completely captures the spirit of the John Williams soundtracks and the melodies themselves are very memorable. I really enjoy the story, characters and puzzles. Despite deaths still being possible in this game, I don't *think* there are dead ends in terms of puzzle design (I could be wrong). The game honestly feels like a nice mid-point between the pre-MI1 and post-MI1 era, in which death is still possible, but you need to make an effort to make it happen, which feels perfect for an Indiana Jones adventure game, to be honest. Fate of Atlantis' only real limitation is the technology it was made with, which is fairly clear particularly now in 2023. Despite that, however, I'm actually very happy to consider FoA canon alongside the movies, which is a remarkable achievement given the difference in format and style, and says a lot about the games' merit as a work of art.
I very much doubt we'll ever see a remaster of these particular games (barring unofficial fan remakes) but one can dream of how the games may appear with an updated visual style and interface while keeping the gameplay intact. When the Lucas special editions/remasters got it right, they got it right. I'd have liked to have seen these games (particularly Fate of Atlantis) get another chance someday.