Protagonist
Character Role Analysis
Romeo
Romeo's name is in the title, a pretty good hint that he's important. His name is also the final word in the play, and he does seem to undergo some sort of change, from lusting after the unavailable Rosaline to being in l-o-v-e with Juliet. So it's definitely arguable that the play is the story of Romeo's relationship with Juliet, rather than the other way around.
Juliet
But what if the play is really all about Juliet? She's the one how undergoes the most dramatic transformation, starting the play as a little girl who says that marriage is "an honor that I dream not of" (1.3.71) and ends as a woman. Unlike with Romeo, the audience gets to see her change every step of the way. After the opening scenes, Juliet also gets some of the play's best lines. And she's the one most often soliloquizing all alone in front of the audience—something done, in most Shakespeare plays, primarily by the protagonist.
If you want to get down to it, Romeo is cute but kind of annoying. Could Juliet's character be the key to the play's dramatic strength and sophistication? After all, the Prince ends the play with the lines, "For never was there story of more woe / than that of Juliet, and her Romeo." Notice how Romeo is secondary to Juliet there?