Instead, the Pirates went with a "safer" pick in a college pitcher rather than go with phenom B.J. Upton, who went No. 2 to the Tampa Bay Devil Rays.
Fast forward to the present day, and history is repeating itself. Call it the Upton Chronicles, redux. This time it is Justin who scouts rave about, and who very well could be the No. 1 overall pick in the draft, unless of course the Arizona Diamondbacks follow the same exact script and go a different route with a college pitcher.
After all, sequels are often not that original.
Regardless of how it plays out, the younger Upton won't be fazed or surprised by any of it. He saw the first movie up close and personal.
"I've seen him go through it before," Justin said about his older brother, now playing for the Devil Rays' Triple-A affiliate in Durham, N.C. "I have a heads up on what's going to be going on."
People looking for a plot line of jealousy, of extreme sibling rivalry, of a lifelong story of one-upmanship, will have to find another subject. Justin sees nothing but positives in his relationship with his brother, from helping him prepare for June 7 to just talking about their games.
"We don't talk about the draft much," Justin explained. "We talk about how he did, how I did in my game and leave it at that. We talk just about every night."
And they don't just pump each other up in good times. Both have had some defensive problems, struggling with throwing accuracy. It's a two-way street, too, with the younger often offering counsel for the elder.
"Whatever we're going through, we'll talk about it and we can help each other," Justin said.
If there's any question about Justin Upton, it's the issues surrounding his defense. While some scouts think he still should start out professionally as a shortstop, others think he should make the move to center field immediately. Either way, no one questions that his bat is what truly stands out.
"He's pretty special. He's got all the tools," one scouting director said. "His future is probably going to be as a center fielder. Right now, he's a little timid defensively, a little erratic with his throws, but he'll go to center and be above-average there and be a big-time impact offensive player."
Given his druthers, Upton would prefer to stay where he's played all his life, in the infield, but he also understands that there may be benefits to moving out to greener pastures.
"I've always been a shortstop," Upton said. "I'd like to play where I'm comfortable.
"But the quickest way to the big leagues will probably determine where I'm going to play. It depends on that situation."
It's another instance in which perhaps he and his brother can compare notes, as many feel B.J. may eventually need to find another home. If he moves to center as well, the comparisons between brothers will continue at the same fever pitch. Many people say Justin might be better than B.J., but it's a contest the Uptons just don't care to enter.
"It depends on who you ask," Justin said when asked who he thought was the better Upton. "We don't look at each other's skills. We look at each other as two baseball players.
"If you ask a scout, you might get a different answer, but to us, we're just two brothers who play baseball."
That's what Justin is trying to focus on these days, just playing baseball. With all the added attention and pressures of being a highly-touted draft pick surrounding him, he's been able to stay focused on helping his Great Bridge High School team capture another title.
"I'm not that anxious [for the draft to get here]," Upton admitted. "I'm really trying to win another state championshhip for my team. I'm just trying to enjoy my senior year."
When June 7 comes around and the Upton family gathers to find out how this draft drama plays out, there has to be at least one small part of the younger brother who would love to be taken in that top spot, just so he can be No. 1 to his older brother's No. 2. Or at least that's how the script should be written.
"It's not really to hold it over B.J.'s head, but I think everybody wants to go No. 1," Upton said.
Jonathan Mayo is a reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.