No need to give too much credit, I'm sure this was talked about many times when 3e launched. I just thought I'd poke the body with a stick come 5e. Glad it resparked your thoughts.
I think many people are over the whole "WoTC owns D&D now???" battle cries of the past. It is what it is. Might as well see what kind of interesting things could come of it.
There are so many directions you could take a game like this for sure. I'm not very up on the HERO system. I'll have to check that out.
Setting wise, there are a lot of options. Mirrodin was the set of cards I enjoyed playing, it had a very Eberron/Planescape kind of feel. You had Myr incubators churning out little "mouser" looking robots. Indestructible Golem creatures, Platinum Angels (which kind of remind me of the Lady of Pain), Weird lion people, rust spells, modular creatures that degrade/increase in power by adding onto themselves (think warforged).
It's a cool setting too.
I could imagine a MTG RPG going like this:
Everyone starts as a "summoner", this of course is not very traditional D&D. "Classes" occur based on schools/colors of magic.
You can only train in one school, or train in multiple schools. single vs dual colored decks. You start with a basic deck created when you build your character. It is always assumed that becoming a "summoner" has givin you a basic set of spells to cast. (think starter decks).
Your character has hit points and mana that require resting to restore. What type of starting mana colors depends on how you built your character/what race they are.
As you explore new lands, you have the ability to gain additional mana from how "in tune" with the surroundings you are. So imagine, you are a dark summoner and you walk into a swamp. You have an advantage, your black mana counts double. Folks that don't train in black magic can only draw non-colored mana.
Cards to add to your deck are given out based on what happens via RPG by the GM. Think pokemon. You make friends with the goblins, you can summon goblins. You get goblin card. You learn protection from Red magic at an academy, you get a protection from red magic card, you find a rare artifact, you get the artifact card.
Possibly, (have to think this out more) cards are played like a spell book, and not at random. Your limiting factor is how much/what type of mana you have left.
Magic cards become treasure/spell cards...this starts to feel a little old school Vancian, but with everyone in the role of "summoner" no one is experiencing balancing issues.
Some cards could be one use only, while others might regen. Perhaps you can keep summoning your new goblin allies, but the Crawl Wurm only comes to your aid once, or the bottle gnome is disposable after drinking his healing elixir.
Down the road, you become plainswalkers where you further specialize your character...
Anyways, there are a LOT of holes in the ideas above. Just throwing some ideas out there to see what sticks.
Hope it helps!
Credit where credit is due: even though I've thought about it many a time- including just using M:tG AS a magic system for a campaign- it was your thread that actually got me thinking about it seriously & practically.
Which is why I'm using HERO instead of some form of D&D.