Nevertheless, have you considered offering "2 versions" of your app?
As you could offer a "Lite" Version which has 1-2 features missing and Ads (including offering to upgrade to the "Paid" version) and a "Paid" Version which has the 1-2 missing without Ads. What is important however, is that the 1-2 features that you remove are essentially bonuses and not core to the operation of the app but rather a nice feature/addition to the app.
With regards to the user experience, just ensure the ads are incorporated into the design/experience of the app when you are creating it rather than making it feel as if they were just added at the end in order to make revenue from the application as this will reduce the affect upon the user experience from a users point of view - Although don't make the ads so integrated that they don't annoy users to pay to remove them (i.e. from your "paid" app) - they still need to be slightly annoying as you will get people paying for your app just so they no longer see the ads.