As someone who loves the X-Men (Nightcrawler and Rachel Summers/Grey are two of my top three favourite super-heroes), this RT score is actually in line with what I expected from this movie right from the outset. The comic book source material honestly isn't the most endearing X-Men arc to me (unlike say the Dark Phoenix saga or DOFP), and the trailers didn't pique my interest. Mystique was never a popular character in the comics, so trying to give her more focus in the movies is a big risk, and honestly didn't work even in DOFP (which was at least somewhat enjoyable, though I didn't like it as much as most). Wolverine is popular, but a large part of this is his interactions with other characters (Xavier, Cyclops, and others), so without them being well established, the "Wolverine is a loose cannon and dangerous" storyline has gotten old really fast.
I really think Apocalypse as a villain was always going to be difficult to do well, since even the comics made his threat level seems way too varied (sometimes a god, other times a normal human threat). His motivations are also tough to relate to for an audience, unless you present him as a "force of nature" instead of as a real character. Kinda like the antagonists in the "Alien" movies. Who cares about the nuance of the Alien's goals...it's all biology/evolution. Apocalypse should be the same (and not even the comics did that right tbh). A comic book movie without a strong villain is going to have issues right at its core as far as the viewers are concerned.