I wouldnt put any Metroid game as a best nintendo game.
Anyways from the following franchises...
Kirby
-Kirby Super Star - A collection of multiple mini games (including Kirby's Dream Land 1) in one package. The remaster on DS enhances the visuals and includes additional content. Revenge of Meta Knight and Milkyway wishes makes this game the best Kirby game and one of the best Nintendo games that isnt Mario or Zelda.
Pokemon
-Pokemon HeartGold/SoulSilver - 2nd gen Pokemon games were amazing due to the amount of content it had (combination of 1st gen pokemon and its locale and 2nd gen pokemon and its locale) - update this on the DS which enhances the visuals and gameplay to play like the 4th and 5th gen games - include additional content. This is like the best packaged experience for Pokemon especially considering the fact that later generations dont even contain the entire pokedex.
Donkey Kong
-Donkey Kong Country 2 - great level design, enemy design and just in general great theme. The variety in level design and style, the great music and snappy gameplay makes this one to be one of the best games from Nintendo. Sadly DKC Returns and Tropical Freeze just doesnt have the same feel to it.
Fire Emblem
-Fire Emblem Awakening - great cast of characters and story. Great entry point for beginners and what revived the entire series with its anime overhaul of a design for the characters. Solid gameplay that introduced an easy mode to make it easier for more people to get into the series. I've played and finished both Echoes and Fates but the story/cast of characters in Awakening imo is the best out of the three.
Edit: About fire emblem, I love the romance/marriage mechanic, I was so into that more than the story lmao. Kinda like how I was more into the social events rather than the main story in Persona 3/4. Speaking of romance/marriage, I remember I beat FE Awakening, the night before my wedding back in 2016. Good times.
(Apologies if my post seems a bit rambling lol)
