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You think protagonsits have to be likeable? Hmmm, that must severely limit what kinds of movies you watch and literature you read.
No, Craig Schwartz in Being John Malkovich was not supposed to be likeable, but a small, petty, pitiful, warped, and selfish individual. High Fidelity's Rob Gordon is a bit of a self-centered shallow schmuck, you bet. It's rather the point of those two narratives. If that somehow hampers you from enjoying the films, I don't know what to tell you.
Here's a brief list of other unheroic, unpleasant, and generally unlikeable protagonists you can avoid: Charles Foster Kane in Citizen Kane, Alex of A Clockwork Orange, Travis Bickle in Taxi Driver, Jake LaMotta the Raging Bull, Popeye Doyle in The French Connection, The Stranger of High Plains Drifter, Michael Corleone in The Godfather films, Allie Fox on The Mosquito Coast, Joe Gideon in All That Jazz, General George S. Patton, and virtually any central character in a Woody Allen movie from Annie Hall onward. BTW, these are also some of the greatest characters, performances, and films you're ever likely to see.
As for Cusack, some other roles similar to Being John Malkovich and High Fidelity you may want to skip are in The Grifters, Bullets Over Broadway, and Tapeheads. Sadly, if you avoid these flicks you'll be missing some of John Cusack's very best work.
If you want to see an all-around more agreeable and likeable character portrayed by Cusack, check out Say Anything..., The Sure Thing, Grosse Pointe Blank, and Better Off Dead - all good movies too. But I think it would be a pity to miss out on the darker side of the guy. But that's up to you, of course.
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"Film is a disease. When it infects your bloodstream it takes over as the number one hormone. It bosses the enzymes, directs the pineal gland, plays Iago to your psyche. As with heroin, the antidote to Film is more Film." - Frank Capra