After reading it for close to 2 decades, I'm a little too close to the material to objectively pick out major flaws. The problems I have with Berserk aren't bombshells or anything. Just little things that bug me occasionally, and three of these are things that will surely be remediated by the end of the story.
I think the pirate boss overstayed his welcome. He was on his fourth rematch with the group by the end [ Vritannis -> at sea (1) -> as sea god appendages (2) -> on the island at night (3) -> assault on the Sea Horse (4) ]. One less would have been easier to stomach, I think. But it's not as if the story revolved around him. He just became the "voice" of the opposition, and so he had to "survive" until that part of the story was done.
I also think that Miura has neglected three sub-characters over the years, at least in terms of their potential: Azan, Puck and Serpico. It's a result of how he chose to balance Guts' new group dynamic (I say new, but it's been this way for a decade now.)
The issue with Azan and Puck is straightforward: they've been relegated to comic relief. This is somewhat understandable with Puck, because he is as old as the series. Miura probably feels like it's okay for Puck to step out of the spotlight and have other characters take the role he once had as Guts' conscience. But it's been a loooooooooooong time since we got a really genuine moment with Puck (the last memorable one was a panel in Vol 27, fearing what the armor would do to Guts). Schierke has basically supplanted the role Puck once had with Guts, and I absolutely love their relationship. So all I'm asking for is more scenes that give Puck more to do as a character than serve as a foil for Isidro's antics.
Azan has been with the group since Ep 278 ("Setting Sail," 2007) but he's had primarily comedic moments -- no sit down with Farnese and Serpico about what happened after Albion. He's still technically pretending he doesn't recognize any of them, even though they have no troubles recognizing him.
These are both big missed opportunities, and I think it's because there's a lot happening all at once with these characters. I do expect some down time in Elfhelm to bring some of these characters to life, but when was the last time Berserk ever
really had down time? (Volume 17?)
Serpico's problem is a bit more complicated... For several years now, he's lacked a clear motivation, which is odd for Miura's characters, since they usually all have very clear-cut motivations. His primary directive in life was protecting Farnese (from herself and from others). But she's grown up quite a bit over the years, and it's resulted in something akin to empty nest syndrome for Serpico (after kids grow up and leave their parents, what are the parents to do?) Combine that with him burying the hatchet with Guts in Vritannis, and Roderick entering the picture, Serpico has been pretty adrift with no obvious inflection point in sight. Now, that alone is not a problem or flaw because structurally, Miura is mid-development for the character. It'd be like complaining about Farnese in vol 23 when she was chafing between her old role and her new one (and people did

). I've got no doubts that there will be something in the future for Serpico that will make sense for his character. It's just that it's taken us a
long time to get there, and it's felt to me like he's been in stasis since that duel with Guts.