Agree with themadmilkman. Don't sweat Thunderbolt, I seriously doubt Apple will abandon something so quickly that it invested so heavily in. More likely that Thunderbolt will be on the Pro line and this new connection will be on the 'book (non-Pro) machines (the same way Apple removed firewire from the last gen plastic macbooks but retained it on the Pros until Thunderbolt was released.)
FWIW USB3.1 seems to perform in the same league as T-bolt (version 1 anyway). Most people don't need anything better than USB3 and have no concept that the difference between, say, a 2.6 and 2.7 gHz processor is meaningless to their word processing and email, or that the difference between USB 2 and 3 makes little to no difference in how long it takes them to back up their spreadsheet work for the day.
I wouldn't blame them if they did though. Like Firewire before it, the Thunderbolt accessory market is sparse and expensive compared to USB. Why make the investment in something few people want? Ihave a Retina MBP and the USB3 HD I have connected to it serves my needs just fine.