It's all a question of level of language (formal English, versus spoken colloquial English). In informal English, all the sentences you wrote are quite natural, and frequently said by native speakers of English. In conservative formal English, however, they would both be considered incorrect. "I wish you came with us" is referring to a past event (which was the fact that you did not travel anywhere to be with us), and should be "I wish you had come with us." (Even if it's over the phone, and the mother is at Fenway park watching a ball game, the action of not coming with us took place in the past.) If you want to refer to the present, you would say "I wish you were with us, it's If you want to refer to the present, you would say "I wish you were with us, it's so much fun."

No, the sentence is perfectly fine as it is. Why did you assume it was wrong? :) The mother is talking about a present situation, over the phone, so "I wish you came with us" is fine.