Earlier quoted context omitted.
The logic is actually simple: If you're trying to plug in a USB device, just plug it in. It'll work, regardless of whether it's TB 3 or just plain USB 3. (update: this is probably for 99% of cases since USB is much more common than TB) If you're trying to plug in a thunderbolt 3 device, it's very likely you know if you have thunderbolt.
Will I? I've seen software developers (tech people!) return their MacBooks to Apple store because they wouldn't drive a Thunderbolt display (with the issue of course being that older MBs had only DisplayPort output, which is physically identical). This will cause confusion (especially with added confusion around DisplayPort standard support over the USB connector) and it's unfortunate that a new connectivity standard…
I'm guessing that they found a pretty decent strategy when thunderbolt took on the mini-dp port and added thunderbolt to the mini-dp connector. Sure there's some confusion in plugging thunderbolt into a mini-dp port, but as Apple was concerned, they were not taking away any functionality, but merely just adding the thunderbolt feature to an existing port.
Apple's potential adoption of Thunderbolt using the Type-C connector would be a similar strategy to the mini-dp/thunderbolt strategy. This finally allows them to unify ports on their whole line up macbook/pro/iphone/ipad/atv/accessories/power/displays, which with their scale would probably translate to a pretty massive reduction in cost for maintaining inventory of the many assortments of ports and manufacturing.
Based on the direction they've taken with the new Macbook and this announcement, It's pretty obvious that this is the direction they would like to go with and lays out the foundation for the expansion of the retina iMac into a retina thunderbolt display.
I'd say it's definitely more of a feature than it is a regression. The world of consumers has shown that it's been able to cope with USB 1 -> 1.1 -> 2 -> 3, with very little pain. For most people it will be the Type-C connector running at speeds varying from 12Mbps, 480Mbps, 10Gbps, 40Gbps... If you have the higher speed, you can supper everything below it (kind of like 10G/40G ethernet). Mac's will probably be sold with 40Gb Type-C ports, iPhones with 480Mb Type-C ports, Retina displays with 40Gb Type-C ports, all with the consumer being none-the-wiser as to whether they are running in USB mode or Thunderbolt mode.