Latex has it's good and bad points.
maintains mental distinction between input and output
maintains a reasonable level of semantic information
reliable and reasonablly fast for large documents
produces really nice typeset output
handles equations well
handles captioning and cross-referencing well
makes a reasonable job at layout before tweaking
only a few image formats work, with traditional latex it's EPS or bust, pdflatex is a bit better but it still pretty limited with PDF being the only vector format supported (which is fun as most pdf creators don't want to create arbitary sized pdfs so you often have to print to pdf then use a seperate tool to remove the borders) and the only bitmap formats supported being png and huffman jpeg (at least in my experiance artimetic coded jpeg doesn't work and gives an unhelpful error message, that caused some head scratching)
the layout engine is reasonablly smart but not smart enough to get a layout i'm happy with without tweaking and the compile-build-view cycle gets annoying during layout tweaking.
the whole system feels like hacks built on top of hacks. The parameters to hyperef to avoid ugly boxes don't work in all versions (not sure if they work in the latest now, I certainly remember having to downgrade when working on my thesis because of this). Hyperref links go to the float caption rather than the float itself unless you add another hack package called hypcap but that in turn requires further hackery to work with custom figure types (such as figures placed by the side of the text rather than inline with it..
table handling leaves a lot to be desired requiring significant manual tweaking for any nontrivial table.
there are way too many markup sensitive characters, this means that significant editing is often required after pasting in plain text.
requires running a bunch of tools in the right order and sometimes multiple times to process a document
Thats my experiance from writing a phd thesis with the thing anyway.