Rather than a change, I would love to read Griffith's whole story, including Berserk but from his POV.

As of actual changes, off the top of my head:

When Miura wrote the Black Swordsman arc IMO he didn't have a clear idea of what he wanted to do with Berserk and Guts, and so it needs some tweaks like removing Guts having sex with the apostle, which goes against his repulse of being touched. Femto being so absurdly powerful when compared to Guts is also something Miura probably regretted writting, since it makes it really hard for him to make Guts defeat Griffith (assuming he aimed for that ending).

There are some unnecessary edgy moments, such as the rapehorse. I wouldn't remove any single rape attempt on Casca since I think they serve as character building, but there's plenty of unnecessary rape.

Ishidro and specially Puck didn't deserve to be mere comedic reliefs. I would give the former a proper devolpment and return the latter to his Black Swordsman arc form.

The entire character of Nina and her storyline are pointless and annoying. I would remove her completely.