Lack of 1st party games, early. Obviously I want new experiences for everyone, but I hope they port some Wii U games too. As somebody who didn't get around to Wii U, I'd love to play Wind Waller again and Mario Maker for the first time.
Lack of 3rd party games. Personally, I buy Nintendo consoles for Nintendo games, but a lot of people aren't content with that. I've seen a post on here called 'what I want from a Skyrim port'. With the unique selling point of the Switch, you'd like to think 3rd party companies will come up with good ideas for their games. However, they'll only do it if there is an audience to cater for.
System storage. As someone who buys games exclusively digitally nowadays, I hope this system is at least 250GB, but ideally 500GB.
Software belonging to your ID going forward. This seems to have already been addressed. I've read an article basically saying 'going forward, games will be tied to the user and their account, not the systems the games were purchased on'. If true, that's huge. Honestly, that's a really good incentive for people to buy Nintendo.