I'll try not to give any major spoilers, but I'm guessing most people here have already seen one of the other versions and/or read the books...
My problems with Part 2:
Why was Geidi Prime outdoors filmed in black and white? There's no such thing as a monochromatic star... not even 8k years into the future.
Feyd also needed a dentist really bad. I really miss Sting for this role.
In both movies, Jessica was far too emotional for her status level and Bene Gesserit training. A major theme of Bene Gesserit training is control of self... similar to the Mentats but different methods.
Chani turned into a real bitch by the end of the movie. I understand some story deviations in each version, but this was too much. In the book, Paul and Chani had their first child before the ending battle. That child was killed by Sardukar during that ending battle.
As far as I remember from the books, all Reverend Mothers drank the Waters Of Life to ascend. Jessica should have already known this. It's how the Reverend Mothers connected with their past ancestors.
I kinda get why Alia wasn't born in this version as it showed Jessica being able to talk with her. They never really explained why Alia was an "abomination", though. (Hint: without a developed personality, past memories could take her over. Being born a Reverend Mother was also a little part of this.) I couldn't stand Alia's creepy voice in the 1984 version, but it was hilarious when she growled with The Voice.
Calling Paul the "mahdi" is very controversial if you understand islam... and not in a good way.
It seems the kangaroo mice are also crack worm poop spice addicts.
The ending battle scene was kinda light for a big finish. At least they didn't pull out the weirding modules.
Paul getting stabbed twice in the knife fight with Feyd was very contradictorial with his training and his developed war time skill set. Paul had been killing soldiers in actual combat for nearly a year. Feyd had been killing drugged prisoners and his staff.
Irulan's final plea with Paul sounded way too desperate for her royal status and Bene Gesserit training. I guess this is the same problem as with Jessica.