That'll work. You can pick one team or the other to write about in the beginning. Like, say, Layton and his company are traveling around when they arrive to the town. Looking for a place to stay, they go to the hotel and see Phoenix and his company in the common room. They don't really meet then, but both sides pay attention to one another (since that's what they do). Once the mystery starts, Layton talks to his company to try and figure out what happened. Phoenix and friends overhear him, and the two sides decide to join forces to solve the mystery.
That's how I picture it happening. You might have something different in mind, but to me, this works better and shows what both sides can do.
i was kinda thinking that while in the hotel Twin A is overcome by Twin B and she takes Flora and Maya (or maybe someone else not in Layton or AA), thinking one of them is her sister.
Then the two parties intervene to help save them both (with a puzzle inbetween) they find Maya and Flora strapped into chairs and Twin B shines a light on them, realizing neither are Twin A, so she runs away and then one more puzzle and they flee from the hotel. (it's about one o'clock, so they try to find somewhere to stay).
They both go to a hotel and stay there (they become friends), then the next morning Pheonix groggily answers his phone, where he finds out he has to defend the woman. The person on the phone (anonymous) states that it's not the girls fault and hangs up. Pheonix takes the job and Layton offers to help him with his case.
Pheonix agrees and they go back to the hotel in the day to investigate.
Some clues they find are;
A diary with different names as entrants;
A photo frame with Twin A and Twin B;
Second Investigation
A phonebook with 'Mum' in it;
The room with the machine;
A safe with the electrical cord used to strangle the father;
"Lady at the funeral words" (where she says a limozine went missing with a coffin in it a day before Twin B's death, the mother returned shortly after with it. Also that the twins death wasn't open casket, which is strange as it is a family tradition of theirs to have it.)
And they find the mothers house and realize that the twins mother killed the father, as what really happened is the mother sold her husbands research and forced him to experiment on the twins. She would say she would murder them as a threat to the father, so he went along with the experiments. The day when Twin B died sent the father insane. When the mother got home she took the father to a mental hospital.
The people at the mental hospital rang and notified the mother that the father had been screaming that: "It wasn't his fault, it was her, she did it!", the mother realised that he meant her and the death of Twin B. So she took her husband out of the mental place for a day and killed him (need to find a way where a clue can be left, i'm thinking she took her back to the place where the experiment took place, strangling him with the cords of the machine). Then on the day before the funeral for the Twin, she took the limozine and placed the body in with Twin B. The funeral took place as planned, no one the wiser.
--
I know i said before the Twin was buried under a false name, but i changed it to she had a funeral, but her father was also placed in the same coffin as her.
I just need some more clues so they don't just take jumps in logic and complete the puzzle with missing pieces.