If you're just searching for tropes, then every character in everything ever is going to trip over something. At some point you just have to accept that characters are going to have characteristics and that doesn't always mean some prejudice or ignorance on the part of their creator.
I mean, calling Jacob on the "Black dude dies first" thing based on one line is pretty disingenuous considering he's survived every one of my playthroughs and does nothing in the game more reckless than any other character. You might have a wafer-thin case if you mention the absentee father, but then family issues are common throughout Mass Effect - Miranda and her dad, Liara and her mom, Wrex and his dad, Garrus and his dad, Samara and her daughters, Thane and his son, Tali and her dad, Vega and his dad. At what point do you call something a theme or a touchstone and stop trying to stretch spiderwebs to join them with an obviously disconnected idea?
You might have a better case with Kai Leng. I mean, I also groaned when he showed up as a ninja, but then I also groaned every time he showed up. But hey, he was handled with aplomb throughout the novels and was actually fairly interesting without being typecast. Yes, he is a ninja, but so is ever other Cerberus agent with Phantom implants. Are all of them Asian? Or are the non-Asian ones guilty of cultural appropriation? It's one or the other. And would it have been better for you if he had been a non-Asian ethnicity using the same techniques? Should Western media never have another ninja-style character just to avoid tripwires? Of course not. Should they handle things sensitively? In most cases, yet. And in Mass Effect's case, they did. Nothing was made of Kai Leng's ethnicity, just as nothing was made of Jacob's background or Shepard's entirely malleable race and gender.
I'm right there on your side in swinging for correct and fair media representation, but at a certain point you have to realize that there's nothing in range for you to swing at. And when you still try to swipe at something at that point, you're just punching at air.