By far the easiest app to use, AdvanceStarter allows you to change the starter PKMN. Any PKMN in the Pokedex can be used to replace the 3 starters. I set mine to "Groudon", "Kyogre", and "Rayquaza".
Start AdvanceStarter.
Use the onscreen instructions.
Your done! You can save your game and test it on an emulator! Thank you for reading and happy Pokemon Game Making!
Of course, you could always take the harder (and in most cases more fun) option of programming it all in code (eg C#) and feeling vary satisfied at the end result