OS
Aside from being as barebones as it gets; Miiverse, StreetPass, the Internet Browser and Activity Log are now gone. There's no built-in achievement system or party chat which have become industry standards, nor is there apps of any kind such as Netflix, YouTube, and Spotify. Nintendo publicly stated friend codes were going to be eliminated but that's not the case, they have made a return with even the most basic of messaging features being nonexistent. Save data can't be transferred in any way, shape, or form. External media such as audio, video, and images can't be accessed.
Accessories
You can debate worth but there's no denying the fact that the accessories are expensive. The feeling is amplified due to competitor items being priced much lower. Everything feels like an additional fee, from Nintendo not including a charging grip or mic with the Switch, needing the HORI Compact Playstand to charge and play your Switch in tabletop mode, to being forced to buy a microSDXC card sooner rather than later due to the paltry 25GB of available storage.
Games
Everything seems to be either overpriced, compromised in the form of graphical fidelity and performance in comparison to competitors, or just simply being a port of an indie game. The few titles that don't fall into this group such as Sonic Mania and Puyo Puyo Tetris are typically handicapped by something such as the the lack of a d-pad. Triple A third-party support is nowhere to be found. The Virtual Console could have helped fill a void but it hasn't been announced as to when it will be available.
Connectivity
You must use a smartphone app to play and communicate with friends. Bluetooth audio devices are not supported.
Online
The online service now costs money with no real value proposition.
Gimmick
It's touted that the Switch comes with two controllers out of the box. Now that I and many of you have experienced it firsthand, there's no way it's more than a novelty. It's just not very comfortable nor is it practical for games with deep meaningful experiences and it's even more frustrating that this was the reason Nintendo removed the d-pad. No one will ever be able to comfortably play a title like The Legend of Zelda: Breath of the Wild, Splatoon 2, or Ultra Street Fighter II: The Final Challengers with a single Joy-Con. HD Rumble will go down as this generations power of the cloud; it's cool but forgettable.
Hardware Issues
The left Joy-Con is having widespread problems causing it to de-sync at random. Nintendo included a dock that scratches your screen after extended use, they also claim if you have a dead pixel on your Switch, it's not a defect. The Wi-Fi has limited range with some being unable to connect to the internet.
I want to love the Switch and tell everyone how great it is. It's a solid piece of hardware and I'm sure their games lineup in terms of first party will turn out great, over time. But I do feel like Nintendo is company run by stubborn old men who are out of touch with reality that take advantage of their loyal fan base.