For me, the main problem is the lack of some features that were really good on the WiiU/3DS. Menu folders, a controller with a built in microphone and audio and I may be one of the few that actually miss the opportunity of having asynchronous gameplay, a feature wich i feel will be welcome on the occasional Switch 2.
Besides that, i miss "Nintendo Selects" discounts in million sellers games. It wouldnt hurt discount games like Pikmin or Fire Emblem for example, that dont have great legs like Mario Kart or Breath of the Wild's, but Nintendo is being very greedy this gen.
They also need to revision the way they're handling their Online service. The way it is now, theres not a lot of reason to buy the expansion pack, as a lot of the games are buggy or ported badly, and the pricing is outrageous, and overall theres just a massive lack of content.