The last idea would be some thematic teams based on the Pokédex holders in the manga. Actually I don't know if you did that already since I didn't beat all the trainers post-game (they're too scary with their lv90 Pokémon ;___
but if you don't, here's the list if you're interested :
Red : Poliwrath (M), Venusaur (M), Pikachu (with Light Ball and Surf)(M), Gyarados (M), Aerodactyl (M), Snorlax (M)
Blue : Scizor (M), Charizard (M), Porygon2 (I suppose he will become Porygon-Z so you may choose that one), Golduck (M), Machamp (M). The sixth Pokémon could be Nintetales (M), Exeggcutor (M), Arcanine, Pidgeot or Alakazam.
Green : Wigglytuff (F), Blastoise (M), Ditto, Clefable (M), Nidoqueen (F), Granbull (F)
Yellow : Raticate (M), Pikachu (like Red's Pikachu)(F), Dodrio (M), Golem (M), Omastar (M), Butterfree (M)
Gold : Ambipom (M), Typhlosion (M), Politoed (M), Sunflora (F), Sudowoodo (M), Togekiss (M)
Silver : Weavile (M), Feraligatr (M), Honchkrow (M), Kingdra (F), Gyarados (M, shiny if possible), Rhyperior (M)
Crystal : Arcanine (M), Meganium (M), Parasect (F), Cubone (Marowak would be fine here)(M), Hitmonlee (M), Xatu (F)
Ruby : Mightyena (F), Swampert (M), Delcatty (F), Castform (F), Milotic (F), Kirlia (Gardevoir would be fine here)(F)
Sapphire : Aggron (M), Blaziken (F), Donphan (M), Tropius (M), Wailord (M), Relicanth (M)
Emerald : Sudowoodo (F), Sceptile (M), Dusclops (maybe Dusknoir here)(M), Snorlax (F), Mr. Mime (F), Mantine (F)
Diamond : Munchlax (Snorlax maybe)(M), Torterra (M), Bastiodon (M), Lickitung (M), Mamoswine (M). Possible Regigigas for the sixth member.
Pearl : Chatot (M), Infernape (M), Luxray (M), Buizel (Floatzel ?)(M), Diglett (Dugtrio ?)(M), Tauros (M)
Platinum : Rapidash (M), Empoleon (F), Lopunny (F), Froslass (F), Cherrim (F), Pachirisu (M)