Of Nintendo's new IPs since the year 2000, which do you think is the best, and why?

From the ones that came to my mind, Splatoon.
Fun and easy to play online matches with a great artstyle. With the first one I played entire days just thinking "one more match and then I go to do another thing".
That never happend.

Edit: Forgot about Xenoblade. I give it to Xenoblade, then Splatoon.

In the case of Xenoblade, I played the four games and loved all of them, althought have not finished the first one.

Started with X and loved the open world.

Torna and 2 made me cried. Specially Torna.

Would it be a stretch to count Metroid Prime as an original IP, even though it's still Metroid?

Saying that, it'd be close between that and Xenoblade, and I'd still lean Xenoblade because I like it more.

Xenoblade games are long but very memorable experiences. Each of the games have managed to blow me away in some fashion, with their scope and general beauty. The only downside is that I can never find time to keep playing them all again.

Pikmin, of course.

Rhythm Heaven

Well, because none of these other games speak to me....Xenoblade.

Animal Crossing, and it's not even close.
Animal Crossing is one my most beloved game franchises. And it's the only ongoing Nintendo 21st Century IP that has become huge. Wii (Sports, Fit, etc.) and Nintendogs were huge, but they've been dead since after the 3DS and Wii U days. Who knows if they'll ever be revived? Animal Crossing is not Mario, Pokemon or Zelda level. But it's a heck of a lot more relevant to most players and consumers than Kirby, Metroid, or Star Fox.
Xenoblade Chronicles is great, but it's an honorable mention and not the main attraction.

Easily Wii Sports.  It was a cultural phenomenon, and I personally had a lot of enjoyment with these games too.

The "new" thing I liked even more this century was Advance Wars, but that IP technically existed in Japan in the 20th century.  To me and other North Americans it was new IP, and it's in my top 10 games of all time.

Lego city! oh hmm.

I couldn't get into any of those titles, not even Xenoblade. I played it for half an hour and put it down, never picked it back up again. Pikmin 3 was fun for a couple hours / sessions. Splatoon not for me (by my kids enjoyed it). Labo robot build still unfinished. Haven't played the rest. But combined we did put in over 500 hours into lego city undercover, close to a 1000 with the 4 of us.

Nintendo, remains Mario and Zelda for me :/

Of all the ones mentioned, Xenoblade is the one Ive enjoyed the most, so thats the one.

Honorable mention: Golden Sun.