I believe the Sandisk 256mb is both a good and reasonably priced atm. As for a 2nd set of joycons, i would recommend a pro controller over the joycons every time. Joycons are small, flimsy and unreliable. There are some good options for carry cases, depending on your requirements. For solely handheld there are some good cases for around £10/$10. If you want to carry everything there are a lot of specialised compartmentalised Switch carry cases but they are obviously a bit more expensive.
As far as games go, you can't go far wrong with a Mario/Zelda/Kart combo. Honourable mentions must go to Mario Tennis Aces and ARMS too, though it's not everyones' cup of tea. I noticed you mentioned Metroid. Unfortunately that has been delayed. It may be an idea to watch Nintendo at E3 to see if any updates are given. There are actually several JRPG's on the Switch. I've seen others recommend Octopath traveller, not got it myself but i would definitely recommend Xenoblade Chronicles 2. Anyway, enjoy your Switch! Although i'm pretty sure you will anyway.
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In my opinion the N64 was not just the best console of the 5th gen but, to this day the best console ever created!
