It does become supremely weird once you reach Children.
And then exponentially so with God Emperor.
I never thought Heretics and Chapterhouse were very interesting or additive to the original trilogy. God Emperor is a very interesting meta-commentary on the first three if you can get into it, though.
The good news is the Sci-Fi series does an excellent job of simplifying the plot of Children and delivering its essential elements without being too weird. Like I said, too, it has an excellent soundtrack and some very good performances from Alec Newman (who was "meh" as Paul and okay as Muad'Dib but then excellent as burnt-out Emperor Paul and even better as The Preacher), Susan Sarandon, and a young James McAvoy.
This paragraph is a good reading of the situation.
The Emperor isn't throwing his lot in with the Baron and Harkonnens. Their "alliance" is one of convenience to eliminate a mutual enemy -- the Emperor wants to destroy Leto and the Atreides, the strongest threat to Corrino rule, and the Baron wants to destroy an ancient rival. The Baron is also well aware of the political crisis brewing over the Emperor's lack of a son. Eliminating the Atreides has the added benefit of removing one of the other potential successors to the throne, and the Baron thinks he's smart enough to maneuver one of his nephews onto the throne by eventually pinning the Emperor such that Irulan must marry one of them. It's the same plan Leto had for Paul, after all, if he could force a political settlement with the Emperor later.
The Baron is very aware how expensive this enterprise will be for him -- a lifetime of income. But he thinks it is worth it to accomplish long-term goals of eliminating the Atreides, the short-term goal of marrying Irulan to a Harkonnen heir, and the long-term dividends of controlling the profits from Arrakis. And its a good plan, really. It almost worked. There were just one or two little things he didn't have in his plan.
There's another whole layer under this regarding what the Bene Gesserit want, too.
These sorts of elements are why I love this series so much. The politics are complex, layered, and realistic, and the characters leading the different factions (Atreides, Harkonnen, Corrino, and Fremen) all have an understandable set of motivations and behave intelligently given what they know and want.
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