You assume that the quake maps were built sequentially, but that's not the case. Since this was all new technology, the "best" maps were conceived at the end of development, after the team was familiar with the tech. You want those maps to be at the start of the game, as it's the first thing the player sees.

Also, the distinct style of the last episode is easily explained by the fact that all of its maps were built by Sandy Petersen. E3 was mostly American McGee, while John Romero and Tim Willits worked on E1 and E2.

I'm not a fan of Petersen's maps either, but they are regarded (and liked) as quite unique, compared to the rest of the game.