In the first example, the comma feels necessary because you're connecting two independent clauses, not because you're repeating the subject.
The two clauses, "Nokia is not your favorite brand" and "it is the best in my opinion," both can stand alone grammatically as simple sentences. This is what makes them independent clauses.
In school, I learned the "comma FANBOY rule" (For And Nor But OR Yet), it's the first comma rule in this guide:
Use commas to separate independent clauses when they are joined by any of these seven coordinating conjunctions: and, but, for, or, nor, so, yet.
The game was over, but the crowd refused to leave.
The student explained her question, yet the instructor still didn't seem to understand.
However, when the two clauses are well balanced, I'd say it's pretty common and widely accepted to leave this comma out. Because of this, I've heard someone call the FANBOY rule a pseudorule.
In your first example, the two phrases aren't well balanced in my opinion. The word is without a subject feels really jarring, even though it is grammatically equivalent to the word are in your second example.