Hmm, I dunno, it depends what timeline you wanna use for MTG...
I could really go for a Dominaria Mod, completely ignoring **everything** after Apocalypse.
I know that the obvious impulse would be to make a Civ for each colour, and maybe an artifact one, but I reckon it'd work much better if we really get into the game world, and make Civs for the bigger nations/factions instead. The 5 colours would fit best as Religions, methinks...
Oa UU: Samite Healer: 0.2, other units on this stack heal 50% faster.
Urborg UU: Sengir Vampire: 10.2, when this unit is damaged, you can disband another unit on it's tile to heal it completely
Yavimaya UU: Maro Spirit: Maro Spirit's attack power is equal to, uh... 10/total number of techs you have
Llanowar UU: Llanowar Elves: Increase production on tiles they are standing
Tolaria UU: Beebles!!!!: Invisible unit, whenever they enter a city, they sabotage production hehehhe

even better, Tolaria UU: Temporal Adept: Consume this unit to reset all units on the map to where they were 3 turns ago hehehehehehhe
or, or, Tolaria UU: Morphling: you win.
*ehem*
aw, there's waaaay too many UUs to be done, and I'm tired...
While we're on the topic though, I think a mod based on more linear, story driven card games like Legend of the Five Rings, or even 7th Sea would be awesome... actually, 7th Sea would make an excellent Archipelago scenario/mod... hmmmm, one ponders...