OS
I agree that it is about as barebones as it gets and that there are some real bummers here like not having Miiverse, an internet browser, activity log, or some media apps such as netflix and youtube, but all of these can be fixed with future patches. It is barren now, but it has plenty of potential and it remains to be seen how Nintendo chooses to tap into that potential in the future. It is only day 2 and it is too early to tell if it will become something ultimately disappointing or awesome. Time will tell.
Accessories
As you said, OP, value can be debated but I agree with you that things are expensive any way you slice it. I personally won't be buying a pro controller until I see it discounted somewhere just because I am fine using the joy-cons but I wish the joy-cons weren't $80 just to get a matching pair of reds. The 32gb of onboard storage is not great but it is a start, and luckily micro SD's are one of the accessories that are not overpriced.
Games
I couldn't disagree with you more here, aside from 1, 2, Switch, I don't think any of the games are particularly overpriced. Zelda is worth every penny and I would argue that Bomberman is too (full disclosure I buy my games through Amazon and enjoy the 20% discount so Bomberman was only $40). The launch library is criticized for having ports, and I'm sure there will be plenty of those, but it's day 2 and I own 4 games for my Switch, Zelda, Bomberman, Fast RMX and Specter of Torment, all but Zelda being currently exclusive (and all of which were fairly priced, in my opinion). I am more than happy to have 4 games at launch and with some promising looking indies, Arms, Mario Kart, Splatoon, FE:W, Mario, etc. all coming out as the year continues, I don't see myself being starved for content in the future.
Connectivity
Lack of bluetooth connectivity is a bummer, and using the app for friend communication is something that remains to be seen, so I'll withhold judgement on that. As things stand right now it's lackluster, but could be patched in the future (I won't hold my breath).
Online
Now, again, I think it may be a little too early to judge whether or not the online is a good value proposition. As of right now it is very barebones, but it is also still free. We don't know exact pricing or what features are still to come. We know there will be a virtual console, and some game rental/online play feature, but not much else. If pricing is cheap enough it could be justified. This remains to be seen and is too early to really make a judgement on (I know, I sound like a parrot at this point).
Gimmick
I don't think the HD rumble or the two joy-con that it comes with is a detracter in anyway. I find the HD rumble to be a clever little feature and the fact that I can essentially split my controller in half to play multi-player games is nice. I can't see any reason why someone would try playing Zelda with a single joy-con (to each their own) when you can play with of them together (is it even possible to play the game with a single joy-con?). Splatoon 2 and Street fighter though, I can see passing a single joy-con over to a friend for a quick couple rounds of multiplayer fun. These may not be the most ideal option but they are more than serviceable for some quick multiplayer. Ultimately, I think it's a neat feature that can only benefit the experience.
Hardware Issues
This where the real issues lie, although I haven't yet experienced it myself (I play relatively close to the console for the most part) the joy-con de-sync issue is concerning, mainly because I am not confident that it can be fixed through simple firmware patches (I would love to be wrong about that) and a revision of the joy-cons would leave early adopters a bit sore. The dock scratching issue is baffling, that this made it through testing is pretty obscene, especially considering how simple it is to fix, there is no excuse for this but with a $10 screen protector and a couple strips of electrical tape, the issue is fixed, for me at least. The underlying issue of it being a thing in the first place is ridiculous and needs some serious consideration from Nintendo to make right. My wifi experience has also been fine, I am right next to my router (which I guess is a bad thing?) and have had no issues downloading content and connecting to the internet but I can only speak for myself in this regard.
All in all, my experience has been a positive one, both docked and as a handheld. I have really enjoyed the console so far but it is only day 2 and I will need a lot more time with the system to see how things evolve and where things go before making any judgments.