Honestly, the reason Tajiri probably disappeared was due to Gen II.
We know the following things
>Development of Red and Green was long and arduous, with Game Freak barely being kept afloat by side projects and nearly going bankrupt several times
>Red and Green have a lot of shoddy programming and are very messy beneath the scenes, being like patchwork
>Gold and Silver began development immediately after Red and Green (whether that's after going gold or being released is unclear) without Game Freak even knowing if the first games were going to do well
>The original vision of Gold and Silver was pretty different to the final product, basically being a different game with a small amount of overlap
>Tajiri promised release dates as early as Fall 1997, but they were constantly delayed all the way up through 1999
>At Spaceworld 1997 in November, they were said to be 85% complete and planned for a Spring 1998 release
>After Spaceworld, Masuda joined the Gold and Silver team after working on side projects like Bushi Seiryuuden, hence why the Spaceworld demo doesn't have new music
>He said that the team and game were in total disarray, and eventually the difficult decision was made to restart development while making use of what worked
>Masuda is credited as sub-director in the final product, and GS are the last games Tajiri is credited as director
>Gold and Silver, while still selling gangbusters, were a noticeable step down in sales from the phenomenon that was Gen I, and Pokémon games entered a little bit of a recession
>Crystal, Ruby and Sapphire, and FireRed and LeafGreen are all directed by Masuda
>Tajiri appeared on GCCX when FRLG were being released to talk about Gen I development, and had at least some hand in the remakes
>DP are the last games he seemed to have made any real contribution to, and I think it was mostly advice
From what I see, Tajiri saw he wasn't totally cut out for video game development and saw what Masuda brought.
