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Smh... a male-female dynamic thru-line is part of the subplot in Die Hard. The male-female dymanic IS the plot of Good Will Hunting. The relationship has a beginning, tumultous middle and an ending that coincides with the plot of the movie. The 2 characters you learn the most about are him and Skylar. You've taken the character development of Will Hunting, snippets of fight scenes and hanging out with his friends, and ignored the movie.
Full disclosure, i was never really a fan of GWH, and i think i only saw it once on video shortly after it was released... so I’m probably not the best person to ask if the relationship aspect was the ‘plot’ or the ‘subplot’... i can tell you that in Jerry Maguire (which i have seen hundreds of times)- the main relationship dynamic, it could be argued - is the bromance/client relationship between Jerry and Rod.. also the fatherly relationship between Jerry and Ray.. not that the Jerry/Dorothy relationship isnt hugely important to the movie (it is)- but it isnt the MAIN thing in my opinion.. Which is exactly why anyone who calls JM a chick flick is a low-information movie-goer, and is engaging in just plain lazy thinking.
And in Die Hard, the ENTIRE reason that the movie works is becuase of the John McClain - Holly Gennaro relationship.. all the explosions and gunfire would fall on deaf ears and make it just another action flick if not for the fact that the film makes us care deeply about the main characters and their marriage.