1. This is an apples vs. oranges comparison because Switch isn't a handheld, but a home console that happens to be portable. As such, the average console owner will buy notably more games and that's visible in the tie ratio where Switch has already exceeded the lifetime tie ratios of all Nintendo handhelds. Of course Switch is a success, there are no two ways about it. We have yet to reach the halfway point of Switch's lifecycle, yet its first party software numbers are already skyhigh.
2. Mario Kart 8 (Deluxe) has the reputation of being the best game in the series, a reputation that NSMB U (Deluxe) does not share. Software quality matters, hence why Breath of the Wild has outperformed Skyward Sword so easily. Switch games aren't going to set new franchise-highs by default.
3. Fire Emblem Fates has each of its paths counted towards the grand total, so its sales are definitely inflated because Fire Emblem fans could get the content of two games for $60 or three games for $80, so an individual Fire Emblem fan contributed up to three copies to the Fates total.
4. 2D Metroid will sell poorly if Sakamoto is allowed to continue to molest the IP. Again, software quality matters. Samus Returns on the 3DS was a 2D game that couldn't be played with the d-pad, to name just one of the things where it went wrong.
Not sure if being "best in the series" means too much. For your last sentence for the bolded, people will mention Pokemon Sw/Sh, since it will likely set itself up to be the third or second best-selling games in the series.
As for your last point, its kinda strange. Metroid Samus Returns was well-received by critics and, outside of a few fans, I've heard mostly good things about it.
Edit: I thought about Ocarina of Time, but it was the best-selling game in the series until Twilight Princess, so my initial point in relation to your point #2 doesn't work out.