Two reasons why you might choose WinUAE or WinUAEX over the real thing:
1) Confugurable controls. You can set your joypad up so you've got 1 button as turbofire, one button as regular fire, and one button as button2. You can even have a button to jump if you like. Try that on a real Amiga.
2) Savestates. Fancy finishing TurricanII in one sitting?