1 I had been to Sydney once, so I chose Melbourne as my next city in Australia’ve already traveled to Sydney so, the next time I visit Australia, I'm going to Melbourne.

"I had been to Sydney once" sounds a little strange. We usually say, "I visited Sydney once," or "I've been to Sydney ..."

2 I have been to Sydney once, so I chose Melbourne as my next city in Australiaalready so, the next time I go to Australia, I'm visiting Melbourne.

Here's another way to say it. Here are more.

- I've gone to Sydney already so, the next time I visit Australia, I want to try visiting Melbourne.
- I've already traveled to Sydney so next I'd like to visit Melbourne.

1 I had already been to Sydney once before, so I chose Melbourne as my next city to visit in Australia.

The originaly makes sense, but it sounds clearer with a few additional words (if that is the meaning you are going for)

2 I have been to Sydney once, so I chose Melbourne as my next city in Australia.

When you say "I have been to Sydney once", you are just making a general statement that you went there exactly one time over the course of your life. For this sentence, "had" is better because you are making a comparison with the second part of the sentence and showing that going to Sydney once happened BEFORE your planned trip to Melbourne.