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I'm looking for a game with pokemon from Ruby/Sapphire/Emerald (Is that 3rd generation pokemon?) with a new storyline. I could go into more depth about what exactly I'm looking for but I'm not sure if this is the right place to post it.
I've found a section in "Emulation" called "Hacks Showcase and a section in "Game Development" called "Games Showcase". What's the difference and where should I look to find proper, finished, working games that I can play through?
Game Development doesn't hack Pokemon Roms and make games out of them. They use actual programs such as RPG Maker or their own client.
If you're looking for Pokemon Rom hacks, see Emulation and Hack Showcase.