The new Mac Pro is the first high end workstation that has ever been made that you can take with you in carryon luggage. That's a big deal. Everything is a trade off, Apple decided to trade form factor for the upgrade cost of the RAM at the extreme high end (128GB), they weren't being too cheap to add extra RAM slots, they needed the space to acheive other design goals.
I'm sure the resale value would be pretty good on a fiber chanel card, regarding SAS, yes the price is $600 vs $300 with thunderbolt, but this is backwards thinking. Thunderbolt interfaces are NOT inherently expensive, they are simply marked up. This is like complaining about how USB devices are marked up too much and trying to stick with paralell ports at the turn of the millenium. A few years from now this argument will be beyond laughable. Apple said they built the Mac Pro with an eye to the future.
Every single benchmark of the dozens I have seen says the same thing. There is around a 5-15% performance hit. If you've seen benchmarks that show otherwise feel free to post them because they would be way out of line with everything else done by various reviewers and I'd be very interested in learning about them.
I will agree that thunderbolt development could improve, especially on the speed side, but I don't think anyone is questioning IF anybody will get around it it, just when and how expensive it will be, and how quickly it will come down in price.
If external bothers you that much, then I propose this solution:
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