This is gonna be a very long response from me! I love researching and reporting! Hah.
Perhaps the most obvious connection, as many have already stated, is the similarity between Team Aqua's and Team Magma's symbols to the Greek letters alpha and omega, respectively.
Here's something I found on Wikipedia: "The Ancient Greek philosopher, Empedocles, held that water is one of the four classical elements along with fire, earth and air, and was regarded as the ylem, or basic substance of the universe."
Water is represented by Kyogre, Earth and/or Fire is represented by Groudon, and Air is represented by Rayquaza.
Water is considered a purifier—a symbol of birth and life. It is vital to all life. All living things are made up of mostly water. Many ancient Greeks, and those of other cultures [and religions] for that matter, believed that the Earth emerged—and thus was born—from water.
There isn't much information about Earth, but again from Wikipedia: "Aristotle, (384–322 BCE), believed earth was the heaviest element, and his theory of natural place suggested that any earth–laden substances, would fall quickly, straight down, toward the center of the cosmos."
Perhaps "straight down" can be interpreted as "down there" (the Underworld), thus indicating the end?
Aristotle also believed that the classical Greek elements had certain qualities: Moist, Warm, Dry, and Cool. Some Greeks called this the Organic Cycle. The first phase of growth is Moist: spring rains, pliant green shoots, rapid growth. The second phase is Warm: summer sun, flourishing individuality, mature vigor. The third is Dry: autumn leaves, inflexible stems, stiffening joints. The fourth is Cool: winter chills, loss of identity, death. Considering this, Aristotle determined that earth was somewhat Dry but predominantly Cool; water was somewhat Cool but predominantly Moist. Notice the connection. Earth has the qualities of death—or end; water has the qualities of life—or beginning.
tl;dr their names may be connected to Greek philosophy, or I could have wasted 30 minutes of my life for nothing. LOL.