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As in you ant there to be three different 'mons to choose from?
I'm not heaps familiar with Emerald hacking, but it should be as simple as editing the script (using a combination of Advance Map and XSE would be the easiest for a beginner).
Just remember, it'll be the Hex number that you want. So, say you want to be able to choose Wooper instead of Mudkip, in the script for the event that you pick the starter you'll have to change the ID for Mudkip (11B) to the one for Wooper (0C2).
Thanks for the help, I should have been more specific, I am looking for where exactly in the code the script for the starters is. I haven't been able to find it, not sure if it's labeled in a funny way or I am just missing it.