We chose to roll with Thompson over Kanter last season, and that decision is even more difficult to defend now than it was then.
Thompson is a good rebounder, has stone hands, and is a mediocre finisher considering the quality of looks he gets as a garbage man - a lot of his shots are right at the rim. He's more switchable as a defender than Kanter is, but he's still well below average on that end.
Kanter is an even better rebounder, has good hands, and is a better finisher than Thompson. Significantly better free throw shooter. He's a substantial negative on defense (you're basically locked into drop coverage of screens with Kanter on the court, and that just isn't viable against some personnel), but again, so was Thompson.
In a vacuum, I think I'd take Kanter over Thompson. Given that Kanter made $5M last season while Thompson made $9M, that choice is even clearer. I acknowledge that we were in an awkward situation early in free agency last year as we waited for the Hayward situation to resolve. But it's a decision that I bet Ainge would like to have back, and apparently, Stevens as well.