Okay, so you think Stockton is overrated and Thomas underrated. I think Stockton is a bit underrated (i consider him a top 5, even a top 3 PG all time, although this new breed of PGs is special) and Thomas a bit overrated. We'll just have to agree to disagree.
As for Thomas playing on one leg in two games, if you're playing, no one cares if you're hurt. No one is completely healthy in the Finals, anyway. They still lost those games despite having a loaded team and a 3-2 lead. Klay Thompson is still playing on a high ankle sprain (similar injury as Isiah Thomas). They won those games. Curry played injured the year they lost with a 3-1 lead and isn't healthy again right now. Injuries are part of the game. If you're playing, no one is going to feel sorry, but the results still count. Isiah lost. Stockton also played well in his Finals appearances. LeBron is going to lose too but no one remembers losing efforts.
And why do you even need someone to "lead" a team on one leg on the Dream Team? The Dream Team is all about the ultimate "team", not hero ball. Playmakers are way more important that scorers. Anyone on that team can score (Jordan, Malone, Barkley, Bird, Drexler, etc.). That's what makes the "death" lineup on Golden State so effective. Everyone can make plays for themselves or other players.
Yes, there are a lot of politics in the Hall. Yao Ming was a great center and worthy of the Hall for all his work in basketball. But he didn't deserve to be first ballot despite having his career cut short in or even before his prime by devastating injuries. He went in right away because he was considered an ambassador of the game and the way he conducted himself on and off the court.
Drazen Petrovic is another example. If he wasn't tragically killed in an accident, there is no way he makes the Hall base on two very good, but not especially great seasons, even if he could have had a HOF career had he lived. He was that special of a shooter/scorer. Laimbeer doesn't "deserve" anything at this point. Every year there are players just as deserving if not more so that don't get selected to the Hall. Not everyone worthy can get in.
But the All-NBA teams aren't generally considered political even if they are picked by the press, requiring some consensus. Stockton made the second team the year before and after the Dream Team. Thomas made the second team in 1987 and not a single selection after that despite a third team being added in 1989. The other guards on the first team right before the Dream Team was selected were Jordan and Drexler.
Magic and Bird were somewhat political selections with Magic coming out of retirement (but it was freaking Magic) and Bird contemplating retirement after an injury plagued season (which he did retire after that season). He did make the second team as late as 1990, so the only forward that was possibly snubbed was Dominique Wilkins as the other forwards (Malone, Pippen, Barkley, and even Mullin) on the Dream Team were perennial All-NBA selections at that time.
Picking Isiah at that time would have been political in his favor, choosing him for his past accomplishments and not what he was capable of in the present. At that snapshot in time (and i can remember the original Dream Team), Stockton was the superior PG. The comparative stat lines for that season weren't even close. Stockton: 15.8 ppg on 11.5 shots and 48% shooting, 41% from 3, 84% from the line, 13.7 assists to 3.5 turnovers, 3.3 rebounds, 3.0 steals, .3 blocks, and PER of 22.8 compared to Thomas: 18.5 ppg on 16.2 shots and 45% shooting, 29% from the 3, 77% from the line, 7.2 assists to 3.2 turnovers, 3.2 rebounds, 1.5 steals, .2 blocks and a PER of 16.0 (15.0 is the league average). So only a few more points from less efficient scoring and everything else outside of turnovers (but a way worse assist to turnover ratio) was worse and some stats about half as much (steals and assists, the all time leader at both).
Stockton also made the All-NBA and All-Defensive second teams that season. Thomas, nothing. Thomas did make the All-Star team (and that is definitely political) that year, but all the best PGs were on the west (Stockton, Hardaway, Kevin Johnson, Payton) compared to just Thomas and Mark Price in the east.
And how does having Karl Malone on your team ensure being able to get 13 to 14+ assists per game for several consecutive years? So should Scottie Pippen have gotten 15 assists per game because he played with Jordan, an even superior scorer? To be fair, the triangle offense tends to prevent gaudy assist numbers, but Thomas had even more scoring options on his team than Stockton with Dumars, Aguirre, Vinnie Johnson, Laimbeer, Mahorn and even Adrian Dantley at one point. No, i don't think there is anything clear about Thomas being better than Stockton, especially during that time.