Two (well, possibly three) big issues with Pages 09 for doctoral theses. One, it doesn't do cross-referencing (especially problematic for footnotes). No cross-referencing? It's 2010! Two, it can't run one footnote across multiple pages. So, if you have a very long footnote (as you occasionally do when writing a PhD), the formatting in Pages 09 cannot deal with it, so you end up with huge gaps, and then all of it on one page. Not ideal. Three, it can be wonky when saving/exporting to Word, especially if you have/need section breaks, tables of contents, etc, etc.
I'm not saying Office for Mac is perfect either; it really isn't (although I'm hearing good things about the 2011 version.) But it still manages to be richer in serious academic functionality than the others, and that is a shame.
Yea Pages seems to be mainly for typing normal, everyday papers, which is why it works for me. I honestly have no idea how my dad uses it for his dissertation haha.