here is an epic case of 'less the more', if your CTR is less that means with less page impressions more clicks are taking place! which is a good thing , indeed a wonderful thing for your bank balance! but the CTR or the click through rate is not the only indice for your revenue potential , along with the CPC and various other factors which will ultimately reflect on your earnings,
i agree with webtechno in the argument that content is the king, as when a visitor is on the site for its content, then even CTR is going to go up ,no matter what, that is basic principle of
seo as far as i know,
also the ads placement and some other things like targetted ads (which is not totally in your hands,maybe somewhat by the tags you supply the bots)