Humbly , before I offer any suggestions and criticism, I have to extoll Emerald Rogue's incredible polish and addictiveness. I can't put this damn thing down; over 100 hours over the past two months! As a result of my obsession, I'd like to offer some ideas that popped into my head that might fit in with the vision of the hack.
Are you playing with someone else's completed save file? Playing with pokemon past gen 3 is unlocked after completing an adventure. There's an entire cutscene explaining where to go, how did you miss that? You're way off thinking this is bad game design. Also I'd say it's definitely a good thing nearly 900 pokemon aren't available from the start. It could easily overwhelm new players, and saving it for post-game rewards the player for playing the game well.admittedly this is a really ugly game design on the developer's part. I feel like it should be automatically enabled, or at the very least making it NOT an unnoticeable secret.