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I'm sure they will! Actually, taking into account the number of golden sun games that have come out recently compared to Punch Out, it's a pretty safe bet to say Isaac will be in it.
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Well, Little Mac was an assist trophy in Brawl as was Issac, so maybe.
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I think out of all the assists trophies (besides Little Mac, now) Isaac would be the most likely as a new character. Maybe Shadow, but if they're really not putting too many third party characters into the game, he may not be.