Well Primarily I chose TESB simply for what it is, the milestone in the legacy and the first real continuation.
Phantom Menace for making me a fan through and through. I found star wars cool until 1999 (was about 10 years old) but when the Phantom Menace came out my breath was simply taken away.
Apart from the nostalgia, I still think that Episode one had the best choreographed sword fight in it (duell of the fates) since there was an actual martial artist in the role of Darth Maul. Besides there's no denying that lightsaber-battles are fundamental in the SW universe and a valid criteria.
Last but not least "revenge", because it's emotionally the most involving film in the saga and happens to show us what we all wanted to see/why the prequels where made-> Anakin's turn to the dark side.
Now I am well aware of the fact that the prequels lack many things that the original films had, especially the acting performance. Yet I've learned to accept them with their flaws and also with their greatness, therefore making 2 of those worthy of "My top 3".