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I think combining both for one huge trade deck could be interesting, but I usually play them separately with one or two mini expansions put in. I find that to be the best balance.
It is interesting. But yes because you don't reliably see most of the deck like with just the base set, some wild things can happen. But that's the beauty of it. The game is still very well balanced though. I think it's a matter of taste in the end, not of balance.