I think some sort of chess clock is a good idea in general.
The implementation should be easy to use and give the players enough time to think but still punish time delay on purpose. It might be difficult to determine a fixed maximum time that is fair. A fixed maximum time also has the downside that at some point a player could foresee that his time will not run out for sure even if he delays on purpose.
So what you think about the following: At the end of the game, if both mages are still alive, the time difference between both players is converted into total amount of damage dealt (need testing for ratio, maybe 2 min=1 damage). The player with the highest total damage dealt wins. If the tie is still not broken, the player with the least time used wins.
For the implementation of the chess timer, I suggest this:
The timer is paused during all phases of the game, unless noted otherwise. In the planning phase, the first player who puts his planned cards on the table starts the timer of the opponent (he cannot switch his prepared cards from now on!). The opponent pauses the timer as soon as he is done with his planning.
In the first quick cast phase, the player who does not have initiative starts the timer of his opponent. If the player with initiative is done with the QC phase, he starts the timer of his opponent. From now on for the whole action phase and final QC phase the timer runs for the player who has turn. After the final QC phase is done, the timer is paused again.
This implementation gives the player with the least amount of time used an advantage in the tie break, which is fair IMO and doesnt favor specific builds. This will also allow to break a tie even if both mages did no damage (e.g. a mana denial build vs mana denial build).
You can say that the use of the chess clock disturbs the game experience, but IMO if this game is going to be a tournament focused game some sort of time control is needed! The player who needs less time to find good actions (who often is the more experienced player) should be rewarded in a tie breaker.
Just thinking about it though. Is it a workable solution? I mean I take 5 seconds to announce I'm attacking you. You then announce your counteres and defenses and stuff, roll defence dice, I've got to get the red dice you were holding from your last turn. you have to (hopefully) find the right damage and status tokens, perhaps fiddle around with moving cards and stuff...
I sort of feel on reflection that theres too much interaction on any one person's turn to say that 'this is your time this is mine' in the same way you might in chess. At the least youd need a much more complex timer that allows players to contemplate their movements on personal time, then pauses to allow for some of the shared administration and card selection.
You got a good point here, maybe the timer should be paused during the action phase in general. Only if one player doesnt react soon because he is thinking (e.g. thinking if he should use a defence), his opponent is allowed to start the timer till that player decided what to do. The same applies if a player starts thinking about which creature to activate or to use his QC marker before activation. Lets say, as soon as a player does not declare some kind of action/reaction after 2 seconds, his opponent has the right to start the clock.