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Yeah, just make it random for a wild pokemon to have either of their 3 possible abilities. Check out src/wild_encounter.c there https://github.com/pret/pokeemerald/blob/master/src/wild_encounter.c#L346 and once the pokemon was created, you could call SetMonData to modify their MON_ABILITY_NUM.
Hey, that was because I had not merged the latest pokeemerald commits. I just updated all my three repos and you should be able to merge all my stuff without any problems.
Small update since many people asked me about this earlier. Hidden abilities are added in without the need of rewriting the structs, I dealt with that. Here's info from the updated main post:
If you're curious, I removed isEgg field from battle pokemon(since eggs cannot participate in battles)...