I agree with "I hope all my wishes come true", if it is a desire for the future. There is a possibility of it happening.
I wish all my wishes came true. This sounds like someone expressing a dream of theirs. There is no possibility of it happening.
I wish all my wishes come true. Repeating "wish" just sounds wrong. For one thing, dreams would probably be used instead of wishes. I would add a would to the sentence:
I wish all my dreams would come true