And story-wise...I would think that today's games should have better writing. I mean, games are a huge industry now, and so, theoretically, the writing talent should be much better (in the same way that game budgets can now bring in big name actors to do voices).
So maybe the answer doesn't lie just in the quality of the programming or writing, but in the execution and the way things just fit, despite the limitations of the genre. Hand-drawn cartoons are "limited" in their ability to depict reality, yet the Disney classics will still stand the test of time no matter how good CGI gets.
Maybe there's just something innately appealing with how adventure games, designed during the technological limitations in the LucasArts era, clicked in our brain. Limits are often good things, especially when it stretches creator and player alike to imagine things outside the boundaries.
Of course, bigger budgets/production quality don't linearly translate to "better" -- Raiders of the Lost Ark vs. Indiana Jones IV (I can't even remember the title of it) is a good example. And there's always the power of nostalgia to exaggerate how good things really were back then...