So let me organize this into a list for what pokemon does what.
Mew- Essentially Adam and Eve of Pokémon
Celebi- Causes forests to grow quicker/heal.
Groudon- Controls hot weather
Kyogre- Controls wet weather
Rayquaza-Controls the atmosphere
Azelf- The spirit of willpower, embodies the willpower of people and pokemon
Mespirit-The spirit of emotions, embodies the emotions of people and pokemon
Uxie-The spirit of knowledge, embodies all that is known about people and pokemon
Dialga-The pokemon of time
Palkia- The pokemon of space
Giratina- The pokemon which balances out Dialga and Palkia
Cresselia-The embodiment of the moon.
Darkrai- The embodiment of nightmares
Heatran- Basically the pokemon of volcanos
Xeneras- The embodiment of life, can create forests when it dies
Yveltal- The embodiment of destruction, kills everything around it when it dies
Zygarde-Balances out Xeneras and Yveltal.
This is just the way I see these pokemon and what I believe they do.