Of all players below 6'4'', Thomas is above average in his one-one-one defense. Players shooting against him average .9% higher than their normal shooting percentage.
There are many players worse than Thomas, but notable starters and sixth men include: Jason Terry, Tony Parker, Russell Westbrook, Rajon Rondo, Kemba Walker, Lou Williams, Mo Williams, Dennis Schoeder, Ty Lawson, Chris Paul, Jeff Teague, Patty Mills, Jeremy Lin, Brandon Knight, Mike Conley, Trey Burke, Ish Smith, Cory Joseph, and Monte Ellis.
I understand that some of those players have to guard the other team's best guard, while Thomas does not, but many of them do not have to guard the other team's best guard. Thomas does often switch onto the other team's best guard. He is right around the middle of the pack as far as the other players normal shooting percentage (meaning he is guarding players who shoot a good percentage, not just the worst shooter on the other team).
He is below average in the number of shots that his offensive player shoots per game (6.7). That is not that much. He is not being taken advantage of nearly as much as Celtic fans would say. Notable players who have offensive players shoot on them more than Thomas with the offensive player shooting better against them than Thomas are: Kemba Walker, Rajon Rondo, Ty Lawson, Mike Conley, TJ McConnell, Darren Collison, Monte Ellis, Mo Williams, Chris Paul, Tony Parker, Jeremy Lin, Brandon Knight, Cory Joseph, Jeff Teague, and Lou Williams (with Dennis Scroeder right after Thomas even though he has less MPG).
His one-on-one defense is better than people think. He forces offensive players to shoot -.1% in shots over 15 feet, where he forces almost 4 shots a game. Players only 2 shots inside 10 feet and 1 shot within 6 feet against him, but they shoot a blistering +10% and +11% against him over their normal percentage. Clearly they have an advantage over him when they do get inside, but that only happens 2 times a game (not including fouls).
He is weak in team defense. Real Plus-Minus really really does not like his defense, as he ranks 76th out of 83 PGs, but still ahead of Schroder, Collison, Vasquez, and Lillard. He is just behind Jeff Teague, Mo Williams, Jrue Holliday, and Trey Burke. He is also ahead of shooting guards McLemore, Waiters, Louis Williams, Wiggins, and Crawford in the stat.
He is still involved with 5 of the top 6 lineups for defensive rating for the Celtics, who are one of the top 10 defensive teams in the NBA.
He is also involved in 5 of the top 6 lineups for a defensive team that is forcing turnovers and a historic rate. He also averages 1.5 steals a game.
Isaiah Thomas has his weaknesses, but I think Celtic fans who watch him every night over-exaggerate them vastly. He is producing like an All-star and if his own fan base does not get behind him, then he won't be recognized like the All-star he is.
Would I rather have enough talent to be able to move him to the bench. Absolutely. But whether he is on the bench or as a starter, he is and will produce like an All-star. Let's support that instead of over-criticizing his weaknesses.