Never thought I'd be the one to come up with this idea, but I already read 2 of those crossover fanfics, and they were pretty terrible. I had to stop reading them at one point because they ended up boring me.
I guess I'd go for something among the recent Scooby-Doo direct-to-video film which also had crossovers, but I never thought I could get this far in sharing it.
The story starts with the gang getting lost as usual, this time from Shaggy misreading the map and they end up in an unfamiliar forest from taking a tunnel. And then they see some familiar creatures, only to Shaggy and Scooby.
Then it cuts to Ash and his friends on their way to Lumiose City for the Kalos League, being near a small town (don't ask for the name), Serena checks her guidebook about the town's history and it tells a story about an evil witch that cursed the place and haunts it to this day. Later at night, when Ash and his friends were staying at a Pokemon Center, Serena hears a strange noise in the woods surrounding the town. Serena goes to wake up Ash, then they go see what the strange noise was. It was then when the witch appeared out of nowhere and ambushed them, Ash and Serena run from the witch but then Serena trips on a small rock, and the witch nearly got her.
The scene transitions to the morning after, when Mystery Inc stop near the unknown builing to ask for a way back. Then a man comes near them, introducing himself as Tom Wilfry warning them to leave or the witch will get them, much to a scared Shaggy and Scooby, then the man leaves. Soon after four kids, one boy wearing a blue jacket, light blue pants, red shoes and hat and raven hair with a creature purched on his shoulder, one girl wearing a pink dress, a red waistcoat, black stockings, brown boots, a red fedora, a blue ribbon tied close to her chest and honey blond hair. Behind them were two siblings, The boy wearing a blue jumpsuit, glasses, and blond hair. The younger girl was a cheerful girl, wearing a brown shirt with a black ribbon, pink shoes, black shorts and a white skirt, wearing a small yellow purse. Shaggy and Scooby recognize them and rush up to them, saying that they've been watching their show on TV.
Shaggy and Scooby were easy to recognize all of them, one of them being Ash Ketchum, a boy from Pallet Town, aspiring to be a Pokemon Master, with his partner Pikachu on his shoulder. Scooby-Doo recognized the honey blond girl as Serena, Pokemon performer and runner-up of the Master Class tripokalon. They recognize Clemont as the leader of the Lumiose gym, traveling with his friends to be more confident, and Bonnie who is dreaming to become a pokemon trainer when she grows up.
Shaggy introduces himself to Ash and his friends, and also introduces Scooby-Doo to them, who the latter greets.
"Hello, my name is Shaggy, this is my best pal, Scooby-Doo." "Rello!" "Hi, Fred Jones." "Hi, I'm Daphne." "My name is Velma."
Ash and his friends greeted them in return, Ash being flattered that Shaggy and Scooby watch his show each saturday. (I like the Pokemon dub. Deal with it.) They then go inside the Pokemon Center and Ash and Serena explain what happened to them last night. Serena explains that last night they heard a noise in the forest and wakes up Ash so they can go investigate. Ash then proceeds to tell that he and Serena went to investigate the noise when a witch suddenly appeared and chased them back, but Serena tripped on a rock and fell, and the witch nearly got her when he commanded Pikachu to use Thunderbolt, sending the witch back to where she came from. He then helped Serena and they both returned. Shaggy and Scooby gulped in fear.
"Well gang, sounds like we've got another mystery on our hands" - Fred proudly announced.
"Wait, what do you mean by that? - Clemont asked him.
"We solve mysteries." Daphne told Clemont. "It's pretty much what you call a profession."
Serena takes her guidebook and does a little research on the teens, who are widely known as "Mystery Inc." where they originate from.
"Wow, so you're mystery solvers!" - Serena said to them.
"Awesome!" - Ash said with his usual determined tone.
"It would be great if you could help us on this!" - Clemont said to the teens.
"Yay, yippee!" - Bonnie cheered.
"We'd be glad to look into this for you." Velma said to the kids.
And so Ash and his friends along with the Scooby gang, go make preparations to go investigate. Serena suggesting they should go to the place where she and Ash saw the witch.
A/N: I don't know if I can go and finish this but I'll just leave it like this so the idea is shown.