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Probably after the elite four they could make it so an extra gym is built for the protagonist? I dunno I feel stealing a gym from a gym leader is kind of mean.....
I think they will leave old pokemon and start a fresh. It would be cool to see new evolutions though I guess.
I count it as a legendary too because it's an interactive pokemon and quite overpowered XD
It all depends on the condition of the box and if the save battery works. Try looking at ebay posts that match the condition of yours. It should go for quite a bit.
If i'm using pokemon ruby and i've made events using poketronic and advance map how do I make it so the event dissapears from the map once you've battled or captured the pokemon?