The difference between using Adalysis, to control your Ad testing, versus relying on Google to optimize the Ad rotation is as follows:
1) AdWords rotation is not always accurate.
2) Google doesn't stop showing your losing Ads. You'd need to know when to remove an Ad so you get the best performance possible. Adalysis will show you when the loser Ad has statistical significance so you know when to create another one.
3) Many advertisers don't just want to optimize by CTR. They also like to test conversions, CPA, or revenue. Adalysis allows you to test metrics such as conversion per impression to ensure that you are getting the most conversions possible (it takes into account both CTR and conversion rate).
4) There are many other features in Adalysis that will give you insights across your campaigns such as multi-ad group testing.