The overall outline for the game is that you've got a commander or leader of some kind that determines a lot of
your base stats for the game - health, toughness, strength, resource income, certain spells or abilities, etc. The
rest of your deck then gives you the ability to 'cast' various allies or creatures, spells, equipment, castles, and
battlefield terrain. Battles would be fought on a grid reminiscent of Heroes of Might and Magic, with your Leader
beginning on the field somewhere on your side, and your opponent's leader on his side.
This seems extremely incoherent.
- If you want a card game in which the Commander deploys units and does useful things by playing cards, both sides should start out on an equal footing, with nothing on the battlefield but identical Commanders differing only in the contents of their card deck. Commander experience should give only cards, not troublesome advantages.
This is the Magic: the Gathering approach: everybody begins with 20 life, 7 cards and nothing else, any difference between players would be an almost unheard of handicap match, and a disadvantage of 1 or 2 cards often means defeat regardless of decks and player skill.
Fixed starting conditions allow players to optimize decks for a single scenario, rather than being forced to do everything (badly). For example, suppose you want to make an all-in aggressive deck (i.e. one that forfeits defense and runs out of resources to kill the opponent with cheap cards before he does much): should it reliably do 15 damage by turn 2, 20 damage by turn 3 or 30 damage by turn 4? Starting at 20 life means that the first deck is too weak, the second is the right target, and the latter is too slow; starting anywhere between 15 and 30 life means that all-in aggressive decks cannot operate properly against most opponents.
- If you want a grid-based, turn-based tactical combat game in which "health, toughness, strength, resource income, certain spells or abilities" of the Commander matter, the Commander is only one unit in the player's army and there's no reason not to begin the battle with more units, their equipments, already cast spells, etc. Cards could still have a role, for example to determine which special combat actions are available, but the CCG aspect would be limited.
A recent particularly pure example: Chaos in the Old World, a strategic game in which Chaos Gods conquer and corrupt regions of the Old World. Every turn, each player spends resources to place units in some region and to play cards from a god-specific deck, which have local effects (one region, or even specific units in that region) and are aligned with that god's specialty and victory conditions (e.g. Khorne, god of slaughter, who scores points for killing others' minions, has many cards to fight more or to win fights).
There is no "commander" (major demons are merely middle-late game expensive units, not leaders) and no deckbuilding (the four gods are already very specialized, while selection and placement of units is the backbone of strategy); cards cause uncertainty and offer an opportunity to make the difference with dirty tricks, putting the right amount of Chaos into what would otherwise be a small scale hybrid of Risk and Diplomacy.