Thanks Siper. The boat is still there as I just haven't gotten to that stage in the hack yet. I plan to make the SS.Anne (or the SS.Whatever) one way to travel to Johto. So it will still be there but you will need some kind of pass which you will receive about a third the way into the story.
Also a note about the beta: There is some story in Viridian which will direct you towards Vermilion, it just isn't there yet.
Disrupter: The Doduo depends. If you have a Pokémon level 3 or lower, then all wild Pokémon will be level 1. I may make the level depend on some kind of average rather than your weakest Pokémon though.
And I don't really have any skills besides scripting and mapping, and I've not built a team yet :/
Edit: You guys got two of the starters yet (No Squirtle yet), and how did you think the side-quests to get them?
And there's another "bug" which I'm aware of. If you get given a Pokémon and you have no room for it, it won't tell you, and it will just be sent straight to PC. It requires a surprising amount of scripting to have it tell you this, and it just wastes valuable ROM space for other things. Anyone who plays any hack ever should know that they get sent to the PC anyway ;)