Atmel Studio 6 is just an improvement in the IDE
Not quite.
AS4 is very simple and has a small foot print, but otherwise a piece of @#$% in terms of its user interface - I wouldn't touch it myself.
AVR Studio 5 / Atmel Studio 6 are based on Microsoft products and totally different interface - those who program in VC should recognize that quickly. The user interface is state of the art, but they are bloated - AS6 is far more bloated than AS5 without offering much to AVR programmers to justify that increase, in my view.
Eclipse is just an ide and can be made to work with other compilers.