I was exactly where you were a 5 weeks ago. The new 6,1 Mac Pro does not look like something I want. The lack of upgradeability was a big negative for me. I felt my 2008 3,1 was not that upgradeable, and I wanted my next machine to be around a long time.
However we differ on the solution. I decided on a new Dual 2.4 GHZ (E5620) Quad core 2010 machine. I felt that the dual CPUs would give the machine a longer life. So far my Upgrades have been:
1. I moved my flashed Nvidia GTX570 from my 3,1 to my new machine, and put the HD5770 in the 3,1.
2. Six sticks of 4GB Ram (new total = 24BGs). The Xeons are three memory CPUs and work best with three sticks (single CPU) and six sticks (dual CPU).
3. Samsung 840 Series 500GB SSD.
4. Apricorn Velocity Solo x2 card for the SSD.
5. I replaced the stock E5620 CPUs with the older but faster W5590 CPUs.
The machine is better than 30% faster than the original machine, and in a couple years when the X5690s become affordable, I may just upgrade the CPUs again.
Your ideas for future upgrades are sound. A RAM Upgrade would be first on the agenda. The Radeon HD5870 is an obsolete card, but the Mac Edition Sapphire Radeon HD7950 or EVGA GTX680 Video cards would be a solid upgrade for you. With the Nvidia card being the better choice if CUDA is important or the Radeon if Open CL is important to you. You may also want to check out MacVidCards store on eBay. He has a great selection of Mac flashed video cards.
Buy a Six Core processor (W3690) in a couple years, when the price is reasonable is also a great idea.
The SSD improves the feel of the machine and really speeds up certain operations. To enjoy the full performance the SATAIII capabilities provide a PCIe SSD upgrade is a must, IMHO. You get the advantages of SATAIII and in addition you get to keep all four internal hard drive bays open for additional storage.
Lou