Maybe I'm missing something - I'm no Google Analytics expert. Here's my reasoning as to why I like Google Webmaster Tools better than Google Analytics ...
For keywords, Google Analytics shows:
- Visits
- Pages/Visit
- Avg. Visit Duration
- % New Visits
- Bounce Rate
Google Webmaster Tools:
- Impressions
- Clicks
- CTR
- Avg. position (SERP)
To me, the Google Webmaster Tools information is more actionable. I have a number of different pages optimized or certain key phrases. I can look at keyword rankings and prioritize SEO. I can spot high impression keywords that I don't have a targeted page for, and create one. I can look at the CTR and see which page descriptions could be tweaked to get a higher CTR. The GA information is interesting, but ultimately not as useful for my needs.