A lot of game designers focus on the story and experience they want to bring, not on the technology the programmers have to use to bring it to life. There are a lot of 'tricks' you can use in a 2d game to let it show more depth (like parallax scrolling, use of angles, lighting etc), so I'm not sure if '3d' means the same thing to a game designer and a programmer.

3d made more dramatic camera work and lighting possible at the expense of increased production cost. The point and click genre always was some sort of niche popular with the tech crowd in the 90's but couldn't scale up when the computer and video game industry broke into the mainstream. I think that is mainly a demographic difference: point and click games are still being made and sold, but compared to the rest of the videogame market they are a niche.