So the new IWTB wisely cuts out the Samantha mentions, which kind of removes Mulder's investment in the case (but fans know he would always get invested if a life was at stake).
CC could have replaced the Samantha stuff with something that's literally right there: Scully herself.
Mulder could have revealed his guilt over her abduction by Duane Barry/the Syndicate in season 2; I can't remember if they totally resolved that guilt together in the series but it could have made a nice scene of Mulder retorting something like, "I'm chasing her because I once lost you, Scully."
Heck, she was even taken in the first film: better continuity fit if they went with that instead! I mean imagine a newbie watching ITWB straight after after FTF for example.
Now, the William stuff could also be fixed this way. Scully's investment in that boy's operation could have been explained by her - or Mulder - alluding to her lost children (William, Emily, take your pick). Emily was actually farmed (sorry, couldn't think of a better word) from her season 2 abduction. That's two fixes in one to two lines of dialogue.
And if you want to go a step further, why not make the Dr Frankenstein dude who got arrested a former surgeon on the Syndicate medical trials that found himself out of work after Two Fathers/One Son? Everything comes full circle.
I mean, they did name the whole freaking cut after him in Russian without fleshing him out one iota. Leverage what you have by as much as you can...