You've just described the current MacBook Pro line - but I suspect what you really mean is change the current line into something that won't sell at all, but will appeal to people who won't actually buy them, but will praise them on forums like this.
I've described the very current MacBook Pro line, but not the near future of it. Believe it or not, most people don't care so much about thickness (judging by the fact that the MacBook Pro sells better than the MacBook Air).
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Thunderbolt is more expensive due to the nature of its engineering. It requires multiple controllers per device, adding up the costs. It has nothing to do with rarity.
Also, it's overkill, meaning why would a vendor bother trying to sell you a more expensive disk using Thunderbolt controllers (requiring the more expensive Light Ridge controller if you want to provide 2 channel daisy chaining) when the less expensive USB 3.0 device provides the same performance since the bottleneck is not the I/O interface, but the actual physical spinning platters inside the case ?
The rarity must be a big factor of it. I can see why FireWire and Thunderbolt would cost a little more, but not by that much.
The advantage of Thunderbolt drives is that you can daisy-chain them together and that TB and FW devices don't use as many computer resources. TB is, of course, great for hubs. They work well for ethernet and digital video, too.