i've been testing heatmap versus CTR theme too.
i have an existing site that's been running for a while with heatmap. Just started running the same site with CTR theme for a few days and it's definitely improved CTR a little
However, the CTR before with heatmap wasn't bad and Heatmap is a far superior theme in terms of what you can do with. CTR theme is a bit of a 1-trick pony - good for basic adsense sites only.
Heatmap on the other hand is in a different league design-wise. it's no slouch with adsense either - i have one site that does around 25% CTR
Let me know if you have any questions
Thank you bougatsa for your feedback.
I honestly don't know what to do because the reaction is very mixed!