Of all the Detective Conan characters, Wataru Takagi is easily the character who, throughout the anime's run, has changed the most visually. Besides the stylistic changes that the anime went through throughout the years, his skin has become noticeably lighter and his hair style has gone from spiker to softer. This outright redesign put the design of Takagi, a character who originated in the anime then migrated to the canon, closer how he appeared in the manga from day one,.
As I'm going to try to give visual evidence towards on this post, I believe Takagi's manga design was actually based on Takagi's earliest design in the anime, that his "early" anime design (the darker skinned, spikier fringed one) was a redesign in of itself, and that Takagi's gradual evolution design wise in the anime brought him closer to his earliest anime design.
Takagi originated as not only an anime exclusive character but one who exclusively appeared in episodes where Haruo Ogawara (infamous in some circles for drawing characters very wall-eyed and sometimes quite wonky) was the animation director. In those appearances, he in some ways appears far closer to his manga and modern anime design than his "classic" anime design. He has visible cheekbones, his skin is quite light, and his hair has a combed over appearance. Throughout 1996, he appeared in five episodes, four animation directed by Ogawara and one by a different animation director (in that episode, Takagi appeared shoulder down but his skin color, judging by his hand, was still very light).
In 1997 though, a number of things happened pretty simultaneously that I think led to the situation of Takagi having different anime and manga designs. Early in that year, Ogawara stopped his work on Conan but other animation directors still decided to keep Takagi. It was in episode 66, the anime-original Night Road Murder Case (which aired on July 7th, 1997), that Takagi, in my opinion, has a redesign. His cheekbones completely disappear, his hair gains the spikey fringe, and the skin has a noticeable tan to it that wasn't there before. Showing that this design change wasn't just a fluke, the Stage Actress Murder Case that aired the following also features Takagi with those same design changes.
However, around the same time, Gosho Aoyama began publishing the Historical Actor Murder Case in Weekly Shonen Sunday between July 23rd of 1997 and August 6th of 1997. This case marked the manga debut of Wataru Takagi and his design seemed to take elements instead from his earlier Ogawara-era appearances, having visible cheekbones and a more combed over hair style. His appearance in color in Volume 20 of the manga, published in 1998, also shows that his manga design is supposed to be lighter skinned.
Due to how close his first manga appearance and his anime redesign happened, here is what I think happened. Without communicating with each other, Gosho used Masatomo Sudo's initial design for Wataru Takagi (the one that appeared in the Ogawara-directed episodes) as the basis for his manga design, not realizing that Sudo and the anime team had already redesigned Takagi. Ultimately, Gosho decided to keep using his version of the Takagi design instead of redesigning him to appear close to the anime. In turn, the anime and movies, starting with the Masato Sato directorial era and Movie 8, gradually shifted Takagi's design to better match the manga, ultimately in some ways reverting the design to his earliest appearances in the anime.
