My Suggestion

Ok, this is my suggestion. It probably fails, but who cares, I'll give it a shot.

You start off in the village of Mercedes Cape. The Professor of the village, (Professor Zeke), is off on vacation in Solcrest City. While on vacation, the Pokemon Lab is empty, but locked. There's a kid living in the house across the street from you who's been your long time foe since childhood. You and him want nothing to do with each other, but when the Atticus Clan raids the village, you and him will have to join forces to stop them. (I know, it's cheesy. ._.) The Atticus Clan breaks open the Pokemon Lab stealing valuable items such as Trainer Kits, Pokedexs, and computers with important data on them. The only thing they didn't steal were pokemon inside a box in the closet. You and your rival are able to choose from 3 different pokemon which are Houndour, Chinchou, and Shroomish. After you and your rival choose your starters you head off to Shifting Falls which is the cave you have to go through to get to Solcrest City to tell the Professor about the lab. First you head off to Route 9001 which connects Mercedes Cape and Shifting Falls.

In the Shifting Falls you and your rival stumble upon a secret hideout inside of the cave. It turns out to be one of the Atticus Clan's secret bases. You challenge the Apprentices that are at the base and after they are defeated, they flee to their other bases. After you head out of Shifting Falls, you battle the trainers of Route 9002 and proceed to Solcrest City. (The trainers pokemon will be levels 4-7). You and your rival tell Professor Zeke about the raid and the hideout and he awards you with the starter pokemon that you chose. He heads back to Mercedes Cape and continues his research when he gets all his stuff back. After all of this occurs, your rival challenges to a battle infront of the Solcrest Hotel where the Professor was staying. He will have a Level 9 starter depending on these scenarios:

If you chose Houndour, he will have a Level 9 Chinchou.
If you chose Chinchou, he will have a Level 9 Shroomish.
If you chose Shroomish, he will have a Level 9 Houndour.

After you fight him you head back to Mercedes Cape to get your Trainer Kit and Pokedex. After that you are free to fight the gym.