All of them, but talking about different time periods. The first one, using "was" implies that he's currently around while "had been" implies he was in the past. With the second and third, he may not be around anymore, or have passed away.

troubled man ? i think you wanna say terrible man..troubled let us feel your dad was dead.

ASALAMALAIKOM. You're a good man. My father was a troubled man. 1. I wish my father was more like you.

1. I wish... was/were... | This pattern is used for a situation in the present, even though the past forms was and were are used : I wish my dad was still alive [now]. I wish my English was better [now]. I wish you were here [now]. 2. I wish...had been... | This refers to a situation in the past: I wish my dad had been healthier [when he was alive], so we could have enjoyed more vacations together. I wish I had studied more English [when I was in school] so that I could understand it today. I wish I had bought car insurance [before the accident happened]. 3. I wish I would have... | I consider this very bad English. 'Would have' is a conditional form and has no place in a 'wish' clause. If I had been younger, I would have married Maria. is correct. However: I wish I would have been younger, so I could marry Maria. is incorrect. I wish I had been younger, so I could marry Maria. is correct

If your dad is dead, or no longer seen as a dad, choose the last two. If he is fine, and you see him as a dad, go with the top one. Because you use the word was - I guess he is dead or better than he was - or you just do not see him as your father any longer.