I am experiencing similar issues with my i7 Surface Pro 3. I own an original Surface Pro (i5) and use the machines as a portable workstation. I primarily work in 3D apps generating content, rendering frames (Mental Ray) and compositing. Most 3D cards (even Intel HD) handle the 3D app interfaces very well, but the machine needs a decent CPU for rendering. The Surface Pro performed well, despite it's small footprint.
In making the jump to an i7 SP3, I had hoped to see some decent performance improvements to go along with the delightful form factor. This sadly has not been the case. Renders are universally slower than my original Surface Pro, running at 50% to 66% of the SP1's speed. Yikes! Mode switches in my 3D apps (where I'm working in moderately heavy scenes) are unfathomably slow as well-- a mode switch which would occur in 3 seconds takes 3 minutes in the SP3.
I'm assuming throttling is one of the culprits here, but I don't know enough about the hardware underpinnings to diagnose the issues properly.
Hopefully MS will address the CPU problems. Having a new top-of-the-line device outperformed by old hardware is both unfortunate and embarrassing in this flagship product.
If anyone knows what settings in the Intel Extreme Tuning Utility might help give the SP3 a boost, I'd love to hear about it. I'm willing to put up with more fan noise if I can recover performance.