PG is a horrible system for level design and you really can't get around that. Even games I like such as Ziggurat have terrible levels because of this.
You can't procedurally generate well made levels that flow smoothly.
>Arent there Rogue-like Mods for Doom anyways?
Yes, but they have the same problems. OBLIGE allows you to generate entire megawads, but those megawads really aren't great.