I've noticed that the motive in todays games and movies resorts to characters who have Daddy Issues and have to fight or kill their father or something else.

Most commonly it is Luke and Darth Vader. I feel other films and games copy off of this.

Tron, had the subject of this guy who gets svcked into a computer program who helps his father in the end.

Lets not forget Serana from the Dawngaurd dlc from Skyrim....with her father Lord Harkon who wanted to make her a sacrifice.

Tidus from Final Fantasy X had daddy issues and had to fight his father, Jecht.

Same with Yuna from Final Fantasy X and X-2, had daddy issues and followed in her father's foot steps.

Solid Snake: big boss or Naked Snake is always repeatedly trying to murder his son as part of a plot to take over the world.

The Lone Wanderer from Fallout 3 obviously had daddy issues and left the vault to find his father; James, although they weren't enemies.

Loki from Thor had horrible daddy issues and felt it was his birth right to have a throne.

They made Buzz Lightyear in Toy Story obviously have daddy issues in Toy Story 2 with Zerg.

So is it just me or is this motive becoming overly used? Why can't there be a different motive for the main character in games and movies?

Well, there's the Oedipus Complex, where the son lusts after his mother and seeks to usurp his father... or hey, there's Oedipus Rex, the trope-namer.

But mostly, I'm guessing a lot of writers have daddy issues.

I agree with fueledbycoffee. I think it's something that has always been around and you're just now noticing it.