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 higher-end 90+W 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.