I had been beating that drum a year or so ago, but if you think about it, Apple has always marketed it's displays to the high end of the market, and in 2016, there wouldn't be many high end resolution-conscious pros interested in a 23.6" or 24" display. Hence, they declined to go this route (although I wish Apple would release a consumer level display in that size with a palatable price point - I think they'd sell a bunch of them). If anything, the existing Thunderbolt Display should have been updated in early-2013 with USB 3.0, updated MagSafe 2, iMac-like thinness, and laminated display. They could have at least sold that at $999 with somewhat of a straight face versus what they sell now.
Looking at other price increases and completely user experience killing decisions, a straight face isn't really a priority anymore. So far this whole shift towards retina/4K/5K/UHD display technology didn't work out as i hoped. From a company, which is highlighting retina screens at every keynote, i expected more than a few mixed messages. After the introduction of the rMBP in 2012, imo this progress slowed down too much. Btw. Apple offers a 4K video recording on the iPhone, but doesn't support 4K on the Apple TV (or via Lightning HDMI adapter). Where exactly should i enjoy those videos? Probably on a 4k/5k iMac with a spinner drive...
Is Kaby Lake officially out of the running for DisplayPort 1.3? I haven't been able to find anything definitive about that. If it did support it, there is a very very slim hope we could see Kaby Lake MacBook Pros at WWDC shipping during the mid-summer months along with a 5K Thunderbolt Display, but as you said, the more likely scenario is mid-to-late 2017 for that setup.
So far nothing official from Intel, but those leaked roadmaps suggested no dp 1.3 and no USB 3.1 Gen2.
Hmmm, so if the fanless enclosure is not the problem, and the Intel HD 515 GPU/Skylake combo supports 4K at 60Hz, and the MacBook's USB-C port has DisplayPort 1.2, than why on earth can it not do 4K at 60Hz? I'm truly surprised that port on the 2016 MacBook isn't Thunderbolt 3 considering Apple has been Thunderbolt's biggest backer since 2011. Shame. I can only theorize that they think buyers of this machine will have very little interest in external displays and super high speed data transfers so why stuff those in there when they are good upsell traits of the MacBook Pros.
zhenya explained the problem and the "negative" consequences very well. Although i tend to disagree about the minimalist vision as sole reason for this decision. Another reason could be up-selling people to a next gen rMBP for a while. Besides that Apple doesn't offer neither a compatible display nor special thunderbolt equipment (SSDs, eGPUs etc) and has currently more to lose (another heat source, less room for the battery, lower margin) than to gain from most of the targeted audience. And yet the lack is still a dealbreaker for me and i wish Apple included it somehow, if it that means adding a few extra grams and millimeters.