The atmels has one advantage (at least for me). You can optain an atmel on these arduino boards. I don't like the arduino "IDE", and i don't use it. I use atmel studio or a simple text editor to write my code, but the boards are great (notably the arduino micro board). They come with all the stuff you need (a voltage regulator, a crystal oscillator, and a uart to usb converter).
You can whack this board into a breadboard, flash your code and everything works fine, which makes life much easyer.