I'll reserve judgement on the new TouchBar, since I haven't had a chance to play with one. I'll say this, though, what they've done is dipped their toe into the fully programmable keyboard space: http://www.geeknaut.com/cool-computer-keyboards-2219350.html
This could be a stepping stone to a fully redrawable keyboard. Not saying I want such a thing, but it's interesting. imagine the entire keyboard surface being the TouchBar? It would suck (I think) for typing, but it would certainly differentiate itself from the iPad, and would start making for custom controls that augment the display.
In some cases I could see this as a better experience than just a pure touchscreen (though it would probably be very niche).
Anyway, even with all of the negatives you mentioned, it's still going to be the best Unix laptop out there. My dream is that HP or Dell find a backbone, and starts pitching supporting and building a perfect Linux (pick any distro really) laptop to devs, or maybe Google makes ChromeOS, that perfect OS. Until then...