I find the key is to mix and match it up. Use both regularly, and you will reap the benefits of both.
I have Crank Bros Candy's on one bike, and Easton Flatboys on the other. Being clipped in helps you to learn a better pedalling technique, and to spin instead of just stomp on the pedals. Obviously it's more efficient too. Using flatties means you don't begin to rely on being able to pull up on the bike to get it airborne, and that you develop better bike handling skills.
I find that having 2 bikes, one with flatties and one with clipless really helps. I never swap the pedals over too, and that's on purpose. Cos that way I force myself to swap between types of pedal dependant on which bike I want to use, which stops the reliance on being on one type of pedal to some extent I find…
Still doesn't make me any good on a bike mind! 😉