It would be a hell of alot more interresting, it's getting a bit repetitive... -_-
EDIT :
The games would be great.
Beginning of game, 3 years ago -was 3 years ago in gsc compared to bryg-, the evil team X succeeded in their plans to take over the world, pokemon trainers were forced underground and only a few freedom fighters remain.
Story : Rid the region of the team, defeating 8 team executives ( instead of gym leaders ), giving you badges after defeating them ( after you got all 8, each they work as a sort of key to unlock a door to the teams hq, defeat the 4 chief executives, then the team leader (instead of the league), then regaining control of the region.
As for legendaries, releasing the previously captured legends, that gave them the power they needed.