When I wrote my thesis, I didn't hack LaTeX - I downloaded the style file and template and just started writing. Someone else maintains those files, and hundreds of Masters' and Doctoral candidates use them without major issues (other than those who've never used anything by Word, but who the hell wants to design for them?)
That person who mastered it? Get them to spend a few dozen hours putting together a bullet proof style. That's how you do it.
Final note: I don't think something built by someone smart can't be improved on. But I do think you need to have a pretty solid understanding of why they did it the way they did before you get to call what you're doing an improvement. And an awful lot of critiques of TeX/LaTeX seem to come from a place of ignorance (frequently the "why isn't it like Word?" ignorance that tend to end the conversation for me).