This will not discuss details of GUI or gameplay. Instead, it will discuss the advantages and disadvantages of the data structures within the file format used by Quake, to find out limitations, and suggest changes. This is a Request For Comment in a sense, as I would like to have my reasoning checked on these issues. Discussion of what I consider drawbacks would be educational, but probably pointless. Note that drawback in this context is not meant with regard to gameplay, but extensibility.
Quake never references the original wadfiles.
I guess that the DOOM engine might well have created a texture froim its patches as soon as it came into view, having either loaded the required patch pixmaps along with the map at startup, or loaded them from file when they were needed. The texture would be kept in memory as long as possible. It seems that it would be possible to introduce an additional step to this preprocessing, enabling the engine to add one or more, possibly semi-transparent, smaller mipmaps to a larger, rectangular and opaque base mipmap. Efficiency is scalable by the number of surfaces actually using this feature. There is a description of NATs on the Editing Info page.