Zelda: Majora's Mask surprised me in that I was shocked we were getting a full-fledged Zelda sequel on the same console in just a 2 year span for the 1st time since the NES.

Paper Mario: TTYD surprised me for its witty story and improved battle system compared to its predecessor.

I was really impressed with the GC hardware-wise and how powerful everyone's favorite purple lunch box had under the hood.. Early titles like Rogue Squadron 2, Pikmin and Melee, and especially games like Sunshine, Wind Waker and Prime really hold up after all these years.

The success of the Wii and the Mario Galaxy titles surprised me last gen.

And the early success of the Switch and how good BotW turned out really surprised me this gen.

My first time playing Fire Emblem.

How Megaman 9 be better than Megaman 2 when Megaman 2 didn't have input lag and had a superior controller for 2D platforming? 

Playing Sm4sh for the first time and realizing that the melee scene is only doing it for the wavedashing at this point.

Playing Breath of the Wild to find that while still overrated, it comes much closer to the consensus of reviews than Ocarina does.

The Switch reveal when I realized that Nintendo was low-key swearing off home-consoles because they've finally understood they're much better at handhelds.

Playing Starfox Adventures and realizing most hate for it is unfounded (it's LoZ with Starfox characters, guys).

Playing LttP for the first time in the early 2000's and thinking "People say this is better than Ocarina?"

((I'd like to add that Breath of the Wild is in my top ten of all time, and my second comment is in relation to how I feel its Metacritic score is a bit inflated; from my personal experience, I'd say BotW is overrated by about 2 points.))

Obviously Eternal Darkness, fist thing that sprung to my mind.