What really comes across so far is that Herbert didn't have a general story arc for the series, resulting in ad hoc developments and a lack of depth.
Frank Herbert did not write series that looked like series. Destination Void, Jesus Incident, Lazarus Effect and Ascension Factor are also very different books connected by being in the same history, but not as a clear progression. Same with Whipping Star and Dosadi Effect. The Dune books could also be viewed as a bunch of different stories connected by one minor character - anyman Duncan Idaho.
No one needs to enjoy this quality to his approach to series; it certainly isn't what we expect of a series and it can disappoint. Heretics and Chapterhouse read more like a single book and are more "fun" in the way Dune is.
Alia has ancestral memories of all previous Bene Gesserits - no, wait, it's actually a molecular memory allowing her to access the memories of anyone she's related to
Just a minor point of order - no one has all the Bene Gesserit memories - in all cases it is either through lineage or Sharing. Paul, Leto, Ghanima and Alia have a mix of lineal memories and Shared memories from Reverend Mothers in that lineage - most recently
Gaius Helen Mohiam, Alia's grandmother, at the moment of Jessica's conception.
I do think that Dune isn't an easy read at all, and that anyone who could manage it wouldn't be put off by the lack of obvious villains in Dune Messiah - at least not to the extent that they would think it was objectively worse for not having them.
It's funny, though, where people's limits lie. It just occurred to me that I've never "got" Doctor Who, and I probably never will.
There are plenty of reasons that people won't like the Dune series. For some it is just a hard slog of a read from Dune on, for other's it is the lack of a series feel (how many series have books that vary in size that much?) or just the fact that Herbert isn't interested in recreating Dune five more times. For him, Paul was a pivotal moment in his future history, and the rest of his characters strenuously attempt to prevent a recurrence. Like real history, the books play out as unique series of events - just like how we haven't had another Roman Empire.
I like all the books because I like what was on Herbert's mind - but he's talking about theories of human interaction that are speculative - like writing a critique of an art movement that has never happened. That's why
I love about SF literature - most SF fans probably do not. I don't really get Gene Wolff - but I wouldn't claim it is because Wolff is bad and his fans are mistaken.