The site of the Acropolis includes all those other "sites" you mentioned and are not separate. They are located on the Acropolis Hill.
The Temple of Olympian Zeus is a few blocks away. I've never noticed it from the Acropolis before. I have gone to that site.
A lot of people buy a multi-site ticket which includes the The Acropolis, the Agora, Kerameikos Cemetery, the Temple of Olympian Zeus, the Roman Agora, the Tower of the Winds and Hadrian’s Library for 30 euros and do the "tour" themselves. Most of the sites are near each other and is very do-able on your own.
Either of the museums are worthwhile with the Archeological Museum out of the main tourist zone. The Acropolis Museum is right across the road from the Acropolis.
There is a lot to do in Athens: the Central Markets on Athinas St. plus all the shops & markets off Athinas St., Anafiotika on the north side of the Acropolis, the Plaka, Psiri District, Changing of the Guards at the Parliament Building and just wandering around. There are numerous other smaller, less-known ancient sites also.
Check out the Athens Guide for more info: