I would prefer a decklock. Just because else luck will play a bigger factor, the ideia of a best of 3 is exactly that with only one game it is hard to decide who really is beter because luck may play a big part in that, in a best of 3 you get more consistency so the chances of luck winning the match are lower.
By changing decks in between you totaly remove this consistency, it now are totaly diferent decks, so you are now just playing bests of one. After the match you still don't know who is beter.. because I might have the best deck in the world, but if my opponent gets the change to perfectly tech against it, he can win easy, even if in his first match he lost.
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