Pretty much everything was telegraphed, and that’s ok — the story resonated with millions of moviegoers and made a lot of money.
Other movies of the era (e.g. Being John Malkovich) didn’t telegraph stuff. That movie didn't win any Oscars and sold roughly 10x fewer tickets.
1999 was a bumper year for film in general. There were too many good picks that many had to be passed over. Eternal Sunshine of the Spotless Mind came out in 2004 to acclaim, and covered similar themes, so it can be done. The casting of Being John Malkovich also made it a long shot for awards, as all of the actors in it are fantastic, but there aren’t any standout roles because everyone in it is so good already, and none of the characters are redeeming in any way, so it’s a hard watch for most folks.
Spike Jonze did get an Oscar nomination for Being John Malkovich, and it was his feature film directing debut. The writer, also in his respective feature film debut (for writing), Charlie Kaufman, also wrote Eternal Sunshine of the Spotless Mind. Ticket sales are the wrong metric for artsy stuff like that, imo.
Ebert said it best:
> Roger Ebert awarded the film a full four stars, writing: "What an endlessly inventive movie this is! Charlie Kaufman, the writer of Being John Malkovich, supplies a dazzling stream of inventions, twists, and wicked paradoxes. And the director, Spike Jonze, doesn't pounce on each one like fresh prey, but unveils it slyly, as if there's more where that came from... The movie has ideas enough for half a dozen films, but Jonze and his cast handle them so surely that we never feel hard-pressed; we're enchanted by one development after the next". He concluded: "Every once in a long, long while a movie comes along that is unlike any other. A movie that creates a new world for us and uses it to produce wonderful things. Forrest Gump was a movie like that, and so in different ways were M*A*S*H, This Is Spinal Tap, After Hours, Babe and There's Something About Mary. What do such films have in common? Nothing. That's the point. Each one stakes out a completely new place and colonizes it with limitless imagination. Either Being John Malkovich gets nominated for best picture, or the members of the Academy need portals into their brains."