Package management is the big one, and the poor integration of BiBTeX/references. A more straightforward way of figuring out clashing packages would be nice.
I also generally disliked how some features were environments (document, abstract figure) whereas others are commands (sections, subsections, paragraphs, etc). Inconsistencies in what things are passed to various commands as options vs. arguments were irritating, and it's always a bear, for example, if you need to pass say math-ey stuff an argument. E.g. \caption{$a+b$} Nope. Can't do it.
I also generally disliked how some features were environments (document, abstract figure) whereas others are commands (sections, subsections, paragraphs, etc). Inconsistencies in what things are passed to various commands as options vs. arguments were irritating, and it's always a bear, for example, if you need to pass say math-ey stuff an argument. E.g. \caption{$a+b$} Nope. Can't do it.