"I hope your wish comes true," should certainly be acceptable. But "come" with no S is wrong.
"is made real" would be the most literal way to translate "se haga realidad", and is also a reasonable present-tense way to translate it. It should be accepted, but isn't, as of Oct 20, 2014.
TIL! haha I found this on wikipedia that agrees with you: https://en.m.wikipedia.org/wiki/English_subjunctive
I hope your wish will come true. OR I hope your wish comes true. Duolingo has a number of similar examples. Those two English translations have the same meaning. In a sentence similar to this, English uses a present or future verb in the dependent clause to express the same meaning, so both translations should be accepted.
Eh. I think conceptually you're right, but in general, Spanish uses more articles than English, so it's a little peculiar to insert an English article where the Spanish didn't have one. (Except with professions, where we say things like, "I'm an engineer," and Spanish says, "Soy ingeniero." But for most purposes, Spanish is more likely to stick in an article than we are.)
Actually hoang is right about the English subjunctive: https://en.m.wikipedia.org/wiki/English_subjunctive