My first impression is politics probably played a role. Did the players/coaches not want Thomas, did the powers that be want a more diverse-looking team? Not that Stockton (or anybody else for that matter) is a bad pick, but surely Thomas would have been a better pick, right?
Thomas was definitely a bigger name at the time. Maybe Carmelo Anthony to Bird, Magic, and Michael's LeBron, Curry, and Kobe?
But if you look at the stats, Thomas hadn't been All-NBA since '87, while Stockton was All-NBA every year from '88 up to to '91 when they picked the team and he was also All-Defense in '91, something Thomas never was once. Utah had a better record than Detroit in '91. If you compare them just in '91, Stockton is better in just about every statistically category (both regular and advanced) other than rebounds.
Stockton led the league in assists and was 2nd in steals.
Also they're picking the team a year in advance (and Isiah was injured in '91 too). So how about the '92 stats/awards as that could help show if they made the right pick or not? Statistically, again it's not even close, with Stockton ahead in just about everything other than points.
And again, Stockton was both All-NBA and All-Defense, led the league in assists and steals, played on the team with the better record, while the only accolade Thomas had was being voted by the fans an All-Star starter.
Thomas was a bigger name for sure. But when you take a deeper look from a pure basketball stand point, I don't think there's anyway Thomas should have been on the team over Stockton or Magic or really anybody unless you want to argue Laettner.