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I've watched David Lynch's Dune, the 3-hour cut (complete with expository animation sequence) and overall I think it holds up pretty well aside from the strong homophobic bent.
However, one of the scenes that bothers me, in fact, the one bothering me the most, is the part of the final scene where Paul makes it rain on Arrakis
Who chose to take this specific diversion from the original novel, and why?
The concept of the rains coming at the end seems to have crept in somewhere between the 6th and 7th version of the script.
In the 6th Draft, the film ends with a closeup of Paul's eye, followed by this scene;
Precisely one year later, the script entered its final revision and this scene was inserted;
284. EXT. ARRAKEEN PALACE - DUSK
Paul opens his mouth and issues an ever increasing wind. Lightning and thunder begin. Clouds begin to form over the Palace. In the half-light of dusk, thousands of Fremen watch the sky. Giant golden lights are illuminated and their rays shoot far into the sky illuminating the growing clouds. Five tremendous bolts of lightning suddenly unleash a downpour of RAIN ON ARRAKIS. The Fremen stand awestruck as they are drenched with water falling from the sky.
The 'who?' of "who came up with the idea?" is pretty easy. The script was written by David Lynch.
The "why?" of "why the heck did they do this" is much harder to pin down. Although I personally suspect that this was intended to portray the words at the end of the Dune novel
"The Fremen have the word of Muad'Dib," Paul said. "There will be flowing water here open to the sky and green oases rich with good things.
As to why this decision (to have it rain) was ultimately taken, the very best answer I can give is Lynch's own words
"this film was my one big failure...it was a nightmare...an absolute nightmare...stupid...awful..."
It is established that the planet can only support spice production because it is dry.
Paul says to the Fremen that they must destroy all spice production on Arrakis.
By making it rain, Paul has accomplished the objective he declared.
By inserting this event into the (1984) movie, it provides a logical ending - Paul learns his destiny, seeks a goal, and by movie's end, he's done it. This makes the movie a self-contained story.
Compare to Star Wars (1977). The very first movie ends with the destruction of the Death Star - a nice neat happy ending which doesn't call for a sequel. Obviously, its commercial success demanded sequels. Empire Strikes Back (1980) ends almost abruptly because it is a given that another installment is to come. Return of the Jedi (1983) again ends with a happy ending to properly close out the trilogy (no further installments contemplated at the time).
Consider also Back to the Future. The first movie was written as a stand alone, despite the hook ending (and the "To Be Continued" which was added to the home video release). The second movie truly ends in mid-story with Doc in the old west and Marty in the 1950s because parts 2 & 3 were shot together.
The studio probably anticipated that Dune would not do well at the box office, and may have wanted to close the door on the possibility of anyone pitching for sequel, hence the nice tidy (rain)bow on the story.
