The original code of Zbrush is a lot of years old. You can spend time rebuilding everything wasting time and the risk of bugs or focus on new features as Pixologic does.
This is not the only program that does that. Max is basically the same program from 1996 with lots of things on top. The difference is that Max was the second iteration of a similar program for DOS and the objective of the 1996 release was to clean the interface and start from scratch, resulting in a rather logical interface.
But if Max was a 3d program in the first release and now is a 3d program, Zbrush was a 2.5 program and now a 3d program, resulting in some inconsistencies in the interface, no matter how cool 2.5 is.
Apart of that Zbrush was already quirky from the start and now continue being quirky. This original way of doing things have given them an edge on how original are creating some solutions instead copycat.