You pointed out some of the reasons yourself.
Not sure PCIe outweighs thunderbolt

unless you have a load of PCI cards that you need. TB can carry PCIe so you still have options if you do need to use existing cards.
That's more theoretical than practical. The bandwidth is highly limited as well. Anandtech could only get 1.3GBps out of their TB2 port, the old MP can do 8GBps out of both of its two 16x PCIe slots PLUS 2GBps (shared) out of its 4x. The PCIe chassis are also cumbersome, have questionable power supplies (as in: what kind of quality? nobody knows), offer no GPU support, and are expensive.
True, you
can do it, but you can't run a 4 port MiniSAS card without an
84% reduction in bandwidth (if it'll run at all).
If there was an option to get a Titan on the New Mac Pro I would have done it straight away for CUDA and Nvidia support but as to the argument that keeps popping up that the GPUs are "2 years old".. what does that actually mean in the real world? isn't the Titan Black based on the GK110 GPU which was launched late 2012? The benchmarks and real world use of dual D700's are pretty decent regardless of the actual GPU chip age, thankfully.
But there
IS an option, that's the whole point. With the nMP, there is no option. As far as chip age, you're welcome to look at the benchmarks and tell me the difference. A single GPU have more power than dual D700.
As to other reasons, the new Mac Pro comes standard with built in HDMI 1.4, Wireless 802.11ac, Bluetooth 4, faster ram, very fast external storage via TB with speeds of over 2000 MB/sec if you need it, partially portable, quieter, more energy efficient etc.
Again, TB's not that fast. Anandtech only got 1.3GBps off of their setup due to the way TB is implemented on the nMP. Even if it were a full 2GBps, you're forgetting the oMP gives you the option of throwing in a controller that supports
8GBps.
As far as HDMI: You can upgrade the oMP's video card, bluetooth, wireless, and storage.
Yes, it's more energy efficient and quieter. So are laptops. For some, this is a huge selling point.
I do like the classic Mac Pro but still stand by what I said because of the above points.
I mostly agree with you, but most of what you're saying ignores the oMP's upgradability due to the amazing power of PCIe and the remainder is a direct result of Apple neglecting the product line. My beef is not with the new technologies like the latest Xeons, wireless, USB, etc in the nMP, mainly just with Thunderbolt and the argument that it's somehow "better" than PCIe--that's entirely dependent on the use-case.
You also mentioned the nMP's use of "future" technology compared to the oMP which I can't argue with, but if you value high powered graphics, the oMP's available options blow the D700 away in most use-cases, and at a lower cost.