There are 2 main things that Google Analytics cannot do:
1. No regionalisation of Search Engines for SEO – this post
2. No automatic tracking of file downloads and outbound links – follow-up post
The first is an major limitation for Search Marketers requiring regional search engine detail for SEO campaigns; The second is a real pain in the bum for webmasters of content heavy websites who need to track non-standard click throughs (file downloads, mailto, outbound links).