I assume by “the story” we mean Uprising? Yes and no. Side note, I had a film critic friend who was actually surprised it wasn’t Hermann because he thought that would have been more of a twist, and on some level I agree with him (though in other ways I don’t). But getting to the film. 

First, why, no, it wouldn’t have changed things:

– Newt and Hermann’s skill sets had gotten so mixed in with one another that, for the purpose of the film, Herman was basically a blend of both Newt and Hermann, a one-man K-Sci lab, and in the personality divorce of their 3-way Drift, all Newt got was the Precursors ;P If it had been the other way around, I think Newt would have picked up some of Hermann’s skills and the only difference would be it’s Newt being the PPDC’s somewhat eccentric tag-along nerd trope and Hermann being the corporate guy who doesn’t really want Newt touching him, I’m not sure much would have changed except we’d be wondering why Newt’s trying so hard to get this guy to like him back?

Basically, for their actual roles in the film’s plot, interchanging them wouldn’t have changed much because they were blended by their Drift. I totally believe Newt could have just as easily fulfilled the Kaiju Blood Rocket plotline, and would have picked up enough of Hermann’s skills to figure out Hermann’s version of the plan.

Yes it would have been different for a few reasons:

– Hermann is just, personality-wise, a far more stereotypical villain personality in the first film (and Burn’s bon structure lends itself to villains, Charlie is just more friend-shaped in general). He’s stern, forbidding, and seems to hate fun. Also Hollywood has a big ol’ anti-intellectualism thing going on so smart = bad. Him becoming a corporate guy working for Liwen Shao wouldn’t have seemed odd at all. A difference would be that he’s difficult for Liwen in other ways, perhaps just saying no to her a lot or being a perfectionist about the Jaegers, saying she can’t have the demonstration when she wants it. (Overall though, I think Liwen would have preferred Hermann even if it meant the destruction of her company and the world itself, because Newt is just a personality that annoys the shit out of her and she got stuck with him for ten years, lol.) 

The tragedy of Hermann being possessed would be there’s even less chance of someone noticing something is up. His brief flash of happiness after they Drifted would appear to be just that: a flash before his standoffish personality resumed. 

It also would have been much harder to convince the audience and everyone in the story that, “It wasn’t him!” that this was something against Hermann’s will I think, because he’s so reserved about his emotions. The only strong argument is that he’d never turn against the cause he fought for, but even Newt would have to admit that most of the time Hermann was a jerk to him and didn’t seem to like people very much. Would it be that hard to see him leap from there to destroying people?

– For “yes it would change things”, I don’t think his ploy would have been the same. I truly do believe the Precursors went into their host’s brain and said, “Ok, if YOU wanted to destroy the world, how would you do it?” and Newt’s answer was, “Duh, take over some evil weapons manufacturer and turn their weapons against humanity. I’d do it with cloned Kaiju brains because that’s my skill set.”

For Hermann, I think it would be opening breaches to let Kaiju back in sooner. Or he’d find a way to make the Jaegers go bad without Kaiju brains, just with rogue programming. Hell, it it was me with his skill set, I’d just have the Jaegers of the world turn on each other and launch World War Three by making it look like nations were turning on one another, then let a bunch of Kaiju come pouring in after the dust settles.

Basically, I’m also not convinced humanity would do as well against Hermann going evil, or even win at all. I sort of have a suspicion that like… Newt’s plan took 10 years because it was silly levels of elaborate on purpose because he was also stalling them as much as possible because he really, fundamentally doesn’t want to destroy the world. I also think his plan is like… kinda dumb and easy to defeat. His specialty as a biologist is just DUMB for destroying the world? 

But Hermann… Hermann’s the robot guy. Hermann’s the math guy. Hermann’s the “learning to understand holes ripped in the fabric of time and space”. I’m not sure the good guys would have even had time to react when his plan went into motion. To quote Newt in TOWOID, “No whimper. Just a really loud bang.”

Basically, the Precursors dun fucked up by taking Newt instead of Hermann, and we’re all lucky they did.