To end re-battles, make sure the condition branch has an "else", tick the box at the bottom of the condition branch, event... Then use a switch.
A few things, I didn't understand the Pokémon bit, is the purple ones, Pokémon you can capture, but they are evolved forms? Didn't see any key to tell me different, that's what I thought.
Most games I've looked at, give me nothing to read, I usually just skim through and read what I want to and if I didn't read enough, I don't comment... But I read almost everything you had put, I checked out the pictures, I didn't download, I'd prefer to wait til I can get further, like gym 3 or something, so I won't judge the game play... I like how this has progression, yet, the progression is unavailable to us, surf/rod and rock smash Pokémon I like that... Shows future prospect when they are available.
You don't need to be a scripter to have a good game, story, game play and events, make the game what they are, you wouldn't believe all the scripts original Pokémon games have, that you don't see, that you probably don't even use... Most implemented scripts are for show really, "just because I can", kind of thing... You don't need to script to make good things either, you can script an entire event, using switches, variables and other even gizmos.
The region sounds nicely worked, however, some of the screenshots don't do it justice... They look, lifeless, but will have to wait and see... Nice to see usages of the day and night encounters, I don't have that in my game, which makes ours completely different, I don't like day and night encounters, I do silly hours at work and I could work from 7am-7pm, how will I ever encounter day or afternoon Pokémon, that's the downfall, not everyone has time on their hands... Let's hope you don't make too many day or night specifics to even the game out a little.
Looks good so far, will keep an eye on this for now, see how things progress, I believe I've helped you with something before, need anything, just give me a shout and I'll see what I can do