The lack of a d-pad is my only gripe.

Can you not change that?

I feel liek the only thing in Breath of the Wild one can change is the Jump button with the run button. I feel like I made that change.

So you coudl change it in Breath of the Wild, if you can't in Splatoon 2. That way those 2 games will play similar for you. I doubt you are playing Splatoon 1 anymore, so that tendency should dissapear after awhile.

So many, but I'll start with the lack of a Virtual Console.

To many games to little time.

No headphone jack in the Pro Controller.

no virtual console, lack of headphone jack in pro controller, and where the hell is netflix,youtube,hulu, etc?

The lack of a proper D-pad is going to force me to buy a Hori controller one day.

Your post sums up my complaints as well. It still feels odd to have a portable device without any sort of video services, especially since the screen is better suited for watching them than any phone or tablet I own. 

Plus, one of my own personal pet peeves is still the relative lack of 3rd-party games. Certainly it seems to be getting better with the recent sports games and Wolfenstein and such, but there are still a boatload of games that could really use ports. South Park would be a great Switch game, for example. I'm not expecting every graphically intense shooter to release for it, but games like South Park would be great on the go. This is likely to improve over the next year, however, so it's not a big problem, just one I hope gets a little better soon. 

I wish the eShop was more fleshed out. It's hard to search through games, and there is no user score or anything to indicate how good the game might be.

My only real gripe is the lack of NAITIVE voice chat without an app. I don't hate the app, just the fact that chat is tied to it.

There are other things that still needs to be added, but this is the only real design flaw I see that bugs me.