[wodenokoto]

Word with Zotero makes for a rather painless thesis writing experience.

Just remember to mark headlines as headings, and don't just change the font size of your headlines. It's easy to insert references to formulas, figures and graphs.

LibreOffice + Zotero makes for the some fairly painless bibliography, table of content, internal figure referencing.

If you need to build advanced graphs from large dataset, there is no painless way about it, but LaTex is in no way more difficult than the other options.