We can blame Robert Wise himself for abandoning the uniform color scheme used in Star Trek: The Original Series (TOS). He thought it would look garish on film.
We can blame Gene Roddenberry for the look for the clothes in Star Trek: The Motion Picture (TMP) as well. He believed that clothes would be disposable in the future -- worn a few times and then recycled -- so all the clothes were designed to look flimsy and uniform in style. "There is no fashion in the future," he said.
Robert Fletcher, an award-winning theatrical costume designer, designed the clothes for TMP. He agreed with Wise that brightly colored uniforms would look unrealistic on film.
There was a mantra during pre-production on TMP that everything "must look real...must look real". 2001: A Space Odyssesy had completely altered the way the public saw science fiction. Gone were the outlandish Art Deco references, garish colors, spandex, chiffon, capes, the "high collar of doom", and glitter. Robert Wise had directed 1971's The Andromeda Strain; as the first big-budget science fiction motion picture since 1969's 2001, it had adopted a starkly realistic visual identity. (The Andromeda Strain had a budget of $6.5 million. Although there had been other sci fi films since 1969 -- Beneath the Planet of the Apes, Escape From the Planet of the Apes, THX 1138, Conquest of the Planet of the Apes, Silent Running, Battle for Planet of the Apes, Westworld, Dark Star, Zardoz, Futureworld, -- they had all been low-budget. A few, like The Omega Man, Soylent Green, Rollberball, The Stepford Wives, The Man Who Fell to Earth, Capricorn One, Close Encounters of the Third Kind, Damnation Alley, and Superman, were set on essentially a present-day Earth. Only two big-budget films -- Logan's Run and Star Wars -- were set in the future. The one which most imitated the pre-2001 style, Logan's Run, failed miserably at the box office. Only Stars Wars, which mixed the "clean look" of Star Trek: The Original Series with an industrial feel -- and which pointedly avoided the garish costumes of the pre-2001 era -- succeeded.
The "make it real" mantra spilled over onto the sets, and this helped drive what happened to the costumes. Nearly all the sets for the film were intended for the TV series Star Trek: Phase II. The bridge developed for Phase II was nearly complete by the time the film was greenlit and the series cancelled, and few changes were made to it. The sets were designed by Joseph Jennings (an art director on TOS), Jim Rugg (FX designer on TOS), and Matt Jefferies (FX and prop designer on TOS). The sets got rid of the neon blinking lights on the control panels, the red turbolift doors, and brilliantly colored images on the monitors. Instead, all colors on the bridge were a neutral gray and matte black, with lots of dull white lights (with no indication of what they were supposed to do or be).
The costumes had to fit, color-wise, with the set design. Fletcher decided to use ultra-washed-out pastels, while trying to retain the "color matches job" scheme of TOS. He chose beige for Ops, steel blue-grey for Science/Engineeering, and dull teal for Command. Another major change he made was to allow only a single badge to be worn on the uniform. On the original series, each duty branch had its own badge on the left breast. These were eliminated in favor of a standard badge (Fletcher used the Command symbol), although the color scheme in the circle behind the "delta" shape varied depending on the duty branch.
Fletcher fabricated a Class A uniform, Class B uniform (for off-duty), and a Dress uniform. The Class A uniform had long sleeves and a circular collar, while the Class B uniform was short-sleeved and had a V-neck drop in the center of the chest. All costumes had the shoe built into the foot, to make it look "futuristic". Fletcher also designed heavy sheepskin field jackets and exercise/leisure wear for the characters.
With uniform design nearly complete, Roddenberry demanded that a "sensor" be added to the belly of each uniform. His idea was that these sensors could monitor a person's vital signs from the ship: A person who was injured or poisoned by a mugatu bite or whatever could be monitored by a physician on the ship, and the ship-board person could relay instructions to a crewmember on the ground. It would also mean that an away-team member could be constantly tracked. (This would eliminate the old trope of "we can't get a transporter lock on him" or "there's too much interference" or whatever crappy rationale was given for not beaming the Captain or Spock out of danger.)
Interestingly, all the costume work was done BEFORE casting was complete. Thus, according to Roddenberry himself, the roles of Decker and Ilia were cast based on how well the actor fit their already-completed costumes. (It was not a given that Persis Khambatta would play Ilia. Although she'd been cast in the role in Phase II, she did not want to shave her head again and was reluctant to do the movie.)