As Alabastron has already mentioned Agios and Elounda are different, and each has their plus points :-) But what they do have in common is that they are both located in a beautiful part of Crete with some amazing views, beaches and of course tavernas too..
Agios has more of a "greek" population being a working Greek town and is "open" all year and caters for tourists during the summer months........with Elounda being more of a small resort that caters more for tourists.
I personally like them both for different reasons and tend to stay between Agios and Elounda, so that I can pick and choose the best bits of both places.
Why not do some searches on You Tube so that you can get a feel for what YOU like on a holiday...I usually do this before travelling to a destination, and always find it a great research tool.
Am happy to give you more specific information about this area, You also didnt mention whether or not you will be hiring a car during your stay ?
Edited: 10:25 am, October 12, 2012