It's surprising how effective a fitness game mixed with RPG elements could be so addictive. One of the biggest surprise IP from this generation easily. 

Don't know if they're gonna iterate on it next generation but it wouldn't too bad to try 

There's a couple of things, but I'll limit it at 3 examples :

- Astral Chain, it's the new core IP from this generation defining that found a somewhat successful base amongst the core gamers of the platform. Stands to become even better with a second game ... Maybe someday?

- The Famicom Detective Club revival. Being arguably one of the most surprising revival for a series that didn't get a thing since the SNES. The remakes of the first two games were already pretty great since the historical value and it's production value(top of the line Adventure/VN) were amongst the best of the genre. Then, they had to surprise us this year with a new entry in the series, which has arguably one of the most shocking story ever told in a Nintendo game (it pulled it off nicely too).
Don't know if we'll anything else from it but this has to be celebrated !

- The Xenoblade series, what else ?
Prior to the Switch, the series had only one game and a port of it and while quite well reviewed, it never found a success to the highs of it's "popularity". This generation changed that. The series ended up in the time of 8 years to get two new acclaimed games, two full campaign expansions, a remake of the original and now the upcoming remaster of Xenoblade X this next March.
All this arguably torpedoed the franchise into the more well known JRPGs of the market, while having a successful growing core on the Switch ecosystem.

Lots of great answers! :)

I think third party support as a whole is probably my #1 most positive surprise. After Wii U, and indeed most Nintendo systems since the SNES, I never expected that the Switch would develop such an extensive catalogue of high quality third party titles, from Witcher 3 to Nier Automata to It Takes Two to Doom Eternal and so, so much in between.

And Square Enix which if you ignore the awful bureaucratic side of their company has released a metric ton of support for the Switch and some console exclusives as well which found success.

Octopath Traveler II being in my top games of this generation certainly helped.

The mainstream adoption of Animal Crossing. I bought the original on Gamecube back in 2002 and fell in love with it. I would always fantasize about one day, the franchise getting the recognition it deserved. COVD and Switch made that possible. It made me happy.

My girlfriend has never gamed in her life. She had seen me playing Breath of the Wild and was slightly interested, mostly in the idea of “collecting sparklies.” I showed her the Animal Crossing reveal in 2019 and within a day she had ordered a Switch online without even telling me. Her first game was Stardew Valley, but Animal Crossing was her salvation during that time and she often says it was one of her best decisions. Many of my friends were scrambling to buy a Switch during that time, oftentimes paying $100-$200 over list price. 

Animal Crossing has always been a gateway game for non gamers, but New Horizons (even without COVID) is a special game that brought so many people into the hobby that we’ll be talking about its importance for gens to come. 

Here’s hoping Nintendo can reach those heights (if not in sales, in fun) with its follow up, which sadly I don’t see arriving until late 2026 or early 2027. 

Another runner up for me would be Astral Chain. At first I thought it looked a bit too "anime" for my tastes, but once I actually tried it, I was blown away by the gameplay and very glad I took a chance on it.  Expectations massively exceeded.

Something I don't think anyone has mentioned, and maybe because it isn't really the question the OP is asking and it's also kind of a "no duh" answer, are the freaking sales of the thing.

I'm shocked! I've been pretty bullish on the Switch for as long as I can remember, as have been most here, but I'm sure there was a time, certainly before its launch, when I was not quite so confident. I don't think I even thought it possible to replicate the sales of the Wii. I know we have the history of the DS to go by, but the DS came out in a time when there were far fewer personal devices to play games on. I mean, it would be years before we even got our first iPhones and androids.

And this time Nintendo did it without leaning into a primarily casual audience, which has paid dividends both in software sales and in brand credibility. I can't remember a time ever when Nintendo's next gen prospects looked so positive.

Metroid remastered, pikmin4, totk

Best positive surprise means the least expected great game to me, so I'll say Pikmin 4. Why?

Because Pikmin 3 on the Wii U was a letdown despite being a good game. It was rather short and lacked good ideas for new features. Part of it may have been that the game had to be rushed out due to the Wii U's software situation in 2013. But whatever the case, it did me make not buy Pikmin 4.

I played the game not too long after release because I could borrow it from my brother (yes, physical copies make it this easy) and was very pleasantly surprised by how Nintendo had adjusted the formula. They took all the good things from the first three games and made them better, plus Otchin is a real winner. Not only as a partner with different abilities, but also because he can be leveled up. This raised the motivation (!) so much for me that I really enjoyed the game throughout despite a bunch of the caves being very reminiscent of Pikmin 2 layouts. I suppose it helped that they removed almost all the annoyances of Pikmin 2's caves (enemies and hazards suddenly dropping in). All kinds of missions along the way to get small rewards on a regular basis while working towards the grand goal were a nice addition too.