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Play 6 counters to auto isn't valuable enough to warrant losing 6 slots in your deck to counter One card. Instead the best answer is to play auto yourself to keep up. This counters are not used.
I like the idea, although it might be a little too powerful as you said. Perhaps there could be an artifact or site to accomplish this, as well… Just one that protects against exchange abilities. There are some new counters to drawing such as Nicanor, The god of this world, and The Priest of Zeus, but I can't think of much that shuts down exchanging.