I recommend making them into a distinct theme so that players can get a feel for the setting and storyline, hopefully creating something akin to a role-playing or storytelling experience. It's also good for them to see the "cycles" between the various decks (such as Dimir Guildgate, Rakdos Guildgate, etc.).
I made five decks, one for each Shard in Shards of Alara. All were designed and playtested to be balanced against each other. I made them into 45-card singleton decks so that players wouldn't see the same card twice in one game. The theme is that the maelstrom is causing the shards to bleed over into each other, causing warfare between the shards as each fights to preserve its integrity from the others.
I also created a super-secret sixth deck, the Maelstrom deck, for use when six people are playing. The idea is that the creatures in this deck actually welcome the conflux and are trying to eliminate all resistance to it. Several five-color cards are herein.
Anyway, in my opinion you're best served by either doing what I did or by following one of these other themes:
- A Khans of Tarkir theme, with one deck for each Khan-Clan (Abzan, Jeskai, Sultai, Mardu, and Temur)
- A Dragons of Tarkir theme, with one deck for each Dragon-Clan (Dromoka, Ojutai, Silumgar, Kholagan, and Atarka)
- An Innistrad theme, with one deck for each race (Human, Spirit, Zombie, Vampire, and Werewolf)
- A Lorwyn theme, with one deck for each tribe (Kithkin, Faerie, Merfolk, Giant, Boggart, Elf, Treefolk, and Flame-kin)
- A Shadowmoor theme, with one deck for each tribe (same as above)
- A Ravnica and/or Return to Ravnica theme, with one deck for each guild (Azorius, Boros, Dimir, Golgari, Gruul, Izzet, Orzhov, Rakdos, Selesnya, and Simic)