Several of your complaints seem to be you just missing visual storytelling and the brief exposition during the worldbuilding segments.

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There are lots of slow moving parts like the arrival on Arrakis with the planning of the departure, the travel, landing, settling in, etc. And then they turn around have them all wiped out in 5 min with no reason as to why (we find out at the end).

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Reasonable complaint about the fall of Atreides, imo. But, this is not an issue with the movie, this is literally what happens int he book. This is one of my main issues with the story itself. The convenience and plot devices used to bring House Atreides down were not clever or impressive.

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I also didn't understand how Paul eyes turned blue by just being out in the dessert for a short time. I thought it would only be after he drank the worm piss.

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It's the Spice that changes their eye color. The worm poison just changed Jessica's immediately. Over time, the consumption of spice changes eye color. This was explained in the movie during the "slow" parts. Seems like you just don't like worldbuilding, or want to pay attention to light exposition.

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There was just so much that was rushed with no explanation. His mom getting all the tattoos on her face with the former old lady didn't have any. Why did the old lady say what have we done when she realized Paul's mom was pregnant. It didn't seem to change anything.

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Agree to disagree on it being rushed. They spent more time on some of this than the book did, and the only way to spend more time on it would be to split this movie into 2, which I'm sure would lead to the same criticisms The Hobbit movies received. As for the tattoos, the older reverend mother did have some, from what I remember. Perhaps look closer. The original reverend mother saying what she said has to do with how the poison would affect the baby. We have not delved deeply into why this can be bad because the daughter isn't born yet. Apparently, there were some changes with her birth and the book readers can explain the reasons why this is a bad thing.

For what is important to the movie, I don't see this as an issue

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At the end the Great Houses arrived above the planet. The emperor is defeated and his treason was exposed. This was the big secret they were trying to keep. Once it is out all the houses just say we don't care and instantly Paul calls for war?

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The fear of the emperor was that the other Great Houses finding out he destroyed one of the greatest of them would cause them to band together to overthrow him. However, this doesn't mean the rest of the great houses would just bow down and accept Paul as the new Emperor. Especially now that he controls all Spice production. It's about power, and I'm sure each leader of each Great House wants to replace the Emperor.

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The original reverend mother saying what she said has to do with how the poison would affect the baby. We have not delved deeply into why this can be bad because the daughter isn't born yet. Apparently, there were some changes with her birth and the book readers can explain the reasons why this is a bad thing.

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Mild book spoilers and it is hinted at in the movie too, its the whole reason Paul is tested with the Reverend Mother's Gom Jabbar at the very beginning.
Any Reverend Mother, or Kwisatz Haderach, can access the ancestral memories of the women (and men in the case of the KH) that are their ancestors. The worry is that the RM or KH will not develop a personality and identity of their own and instead be overcome by a strong presences in their ancestry. That strong presence could completely control the child. This was an Abomination is according to RM. This can be especially dangerous if you have someone like the Baron Vladimir Harkonnen as a grandfather.