My advice: Base with SSD beats middle without.
If the extra $200 or so means nothing to you, and you plan on an SSD anyway, get the middle (3.5 GHz) model, mostly for the GPU, which has a higher percentage performance difference than for the CPU.
However, Apple is charging a LOT for these slight upgrades compared to the component cost differences. They want a "good, better, best" differentiation, and the middle one is better in only minor ways. The difference in cost between the two CPU's is maybe $10-15 or so, and similar for the GPU. It's the Apple tax in high gear for these minor changes.
These two models should produce no noticeable real-world differences. Benchmarks and perhaps a few certain long, hard production runs (transcoding, etc.) will still only be a few percent different. Heat will be slightly higher for the middle model, but probably not very noticeably. (No, the base model will produce less heat; the TDP numbers are for worst-case maxed-out temperature tolerance for setting throttling points, and not a measure of actual power used.)
In my case, I went with the base model (with 512GB SSD) because I was more concerned about any increase in noise than I was about a slight performance advantage. I would have been more unhappy if the noise was higher with the middle model than I would have been if the performance was slightly lower with the base model.
The other thing about the base model is that, for many people, saving the $200 or so can help you to upgrade to an all-SSD system, which has large advantages in speed and lower heat, noise and vibration. Do that!
In the end, the base model (with SSD) is a very snappy system whose fans rarely if ever budge from their minimum speed. Games at 1920x1440, with maxed out detail and anti-aliasing, etc., seem to run at full frame rates (locked to 60 Hz in all models) with no throttling and minimal if any increase in fan speed. (The "K" chips will definitely run a lot hotter - for some that will be OK.)
These are nicely improved machines in many respects. You can't go wrong with any of them.