How to include incremental research in the thesis
From the point of view of the reader, jumping to the most sophisticated version of a method can be difficult.  A thesis isn't a textbook, but there are parallels.  A textbook often uses an incremental approach starting with almost a toy model to get the basic concepts sorted, before making it more realistic.  The assumed background knowledge of someone reading your thesis might let you skip the first step but not necessarily (don't write just for the examiners). It also allows you to indicate why you made certain decisions in the final version.