Interesting topic. But it's hard to say. EAD1 made some of the ones that stand up to the test of time really well. But EAD4 did a fine job with NSMBW and NSMBU, "fine" in the sense that I think they contend with and succeed their older brothers 3 and World.
Tokyo is an odd one. I couldn't believe it when I found out 3D Land was from the same studio that made the Galaxies. I suppose the specific teams might have varied, it's just that Galaxy has some strange decisions made for them that 3D Land fixed, and World is improving upon... but then, I thought Galaxy 2 was a great improvement over the first, so they're just getting consistently better at what they do, and that's nice.
Intelligent Systems is responsible for some big ones. Tetris Attack is one I love very much. Paper Mario goes without saying. WarioWare is the [dukar]. But... is it all over for them? It's been a long time since Smooth Moves and a longer time since Thousand-Year Door. Uh-oh.
Funny the article's only comments on M&L are that it's more childish and upbeat. The words I would use to describe PiT are "needlessly macabre".