The short-comings are:
- Outline mode: MS-Word has outline mode, which lets you move whole sections of your document around via drag'n'drop which I found critical for getting the basic structure of the document in order. With Google Docs you can cut'n'paste sections, but it's hard to get the structure, especially when considering short-coming #2 which is...
- Outline numbering: While Google Docs does support having a table of contents, it doesn't support outline numbering of sections. (I did find this bookmarklet which will do it for you, but you have to run it every time you change the sections.)
- Image captions: While MS-Word makes me want to pull my hair out at times when it comes to image placement and Google Docs has a nice drag it where you want it interface, it has no support for image captions.
- Bibliography and Citations: Again, MS-Word is far from great, but Google Docs has no support. Though it looks like you can post-process this (see second paper below).