Technicality: all tablets use eMMC since SSD is too big for them.
That said, it is not the form factor that dictates performance because you can have high end eMMC being faster than cheap SSDs. It all depends on price, but yes in general eMMC is slower due to less energy consumption
If performance is your #1 goal, you would not go from an i5 Ivy Bridge (in the original Surface Pro) to the Atom (Cherry Trail).
And all Surface Pro machines (1, 2, or 3) have true SSD. Only Atom machines and cheaper machines/tablets have eMMC.
Of course, if other factors are important, then the Surface 3 can come out ahead. I use my Surface Pro 2 as my primary PC. It doesn't do the heavy duty video encoding for Adobe Premiere or Handbrake which is reserved for my desktop machines. But all my work, my video editing, my photo editing, etc. is all done on my SP2. There's no way any of my workflow can work on an Atom. That's just not what the Atom is meant to do. The Atom is meant for things a typical consumer does (web browse, type some documents, watch some videos, play some games, etc.).
Now, if the trackpad is unusable to you (my trackpad on the SP2 is pretty much worthless) and you don't want to deal with a mouse or trackball, then you'll like the trackpad of the Surface 3 which is much better.
Also, you are correct that the single kickstand position of the SP1 is awful for the lap. I love my SP2 because of that second position which makes it totally comfortable on the lap for me. And the Surface 3 has 3 positions now.
Again, it comes down to how much you value performance above the other factors. I know compiling code, editing video, editing photos, etc. can be quite a chore on a CPU like the Atom or even the i3 (which is faster than Atom).
I can see going from SP1 to Surface 3 because of the SP1 limitations as long as performance on the Atom is okay to you.
For myself, there's absolutely zero chance of going from SP2 to a Surface 3. SP2 is a very good improvement on the SP1 (better CPU, more kickstand positions, better battery life, slightly better screen, etc.). And the SP2 is the fastest Surface Pro under sustained load. Faster than SP3 due to SP3 throttling and because the SP2 only has to drive a 1080P screen versus the higher resolution of the SP3.