Well after mulling it over, I came up with this:
This story will take place during the time of the D/P/Pt arc. Since we don't know what the Dex Holders are doing while Dia, Pearl and Platinum are adventuring in Sinnoh, this fits perfectly.
Red, Green, and the other PokeDex Holders of Kanto have come to Hoenn on order of Professor Oak to investigate an odd weater-related phenomanon. Gold, Silver, and Crys are in Hoenn for the same reason, but in order of Professor Elm. Ruby, Sapphire, and Emerald have also been informed about the odd weather occurance and have been ordered by Professor Birch to meet with the other Dex Holders in Lilycove City.
The cause of the phenomanon is that Rayquaza has abandoned Sky Pillar and has been using its powers over the Ozone layer to cause freak storms and twisters. Why Rayquaza is doing this is unknown at the begining of the story, but is revealed later on.
Meanwhile, in the outskirts of Fallarbor Town, Mewtwo is training to master the ultimate Psychic-attack, Psycho Burst. Here he encounters Deoxys, but their confrontation is not explained until later. All that is disclosed is that Deoxys is in Hoenn for an important mission.
Giovanni and TR seem to be seperated as Giovanni is traversing Hoenn on a tip from an anonymous source to find his son Silver once again. TR, on the other hand, does not seem to be acting on his orders. They seem to be under the leadership of an unknown person, but what exactly they are doing in Hoenn is unclear until later.
The relationship that evolves throughout the story will either be Green/Blue, Silver/Gold, Ruby/Silver, or Ruby/Sapphire. It will begin very subtle regardless of the coupling (description of blushing, stuttered conversation) and will be clearly established by mid-story (X protecting X from an attack, X having a tender moment with X)
The abandoned laboratory will hold a startling realization for the protagonists. The dangerous Pokemon lurking inside is one who was experimented on by both Team Magma and Team Aqua before they broke up.
The character who dies will either be a Gym Leader, Elite 4 Member, or PokeDex Holder. How they die will be kept secret, but it will occur near the story's end.
If you feel like battling, send me a message (: I do use hacked Pokemon and am not afraid to admit it. If you have an restriction (No DW Pokemon, no legendaries, etc.) I'd be happy to oblige by those rules.