If I could, I would implement a 'Yes' option like this:
- "Yes, you'll join us? Alright! Meet me at our hideout in Celadon City!" (Vanishes)
- Game continues as normal, pesky Snorlax and guards meaning you have to go Cerulean-Vermilion-Cerulean-Lavender-Celadon.
- Enter the base "welcome, new recruit!" (shows you down to the bottom level)
- "Now, we'll just take your Pokémon in exchange for our standard Rattata and Koffing team"..."What's that? You don't want to give up your Pokémon?"..."Well do you want to join Team Rocket or not?"..."No?" (Attacks)
- You fight your way out of the base instead of into it.
- Game proceeds as normal, with that wonderful Gen I/II feature of choice in the order in which you grab gym badges. So much better than Unova's one-way system!