The main reason for preference for CDA sectors is that these are located in zone I which is still regarded by people as the 'real' and 'posh' Islamabad.
Otherwise, you can see that zone II CDA sectors like I-14 and I-16 are lagging behind private societies of zone II like JKCHS and Multi-Professional.
The reason is simple, CDA has lost at least half of its previous credibility because of lack of funds (which is preventing CDA from proper maintenance of those of its sectors where there are no VIPs) and misplaced priorities. Nowadays most of CDA work and money is being spent on very good maintenance of VIP sectors in zone i but middle class sectors especially in zone ii like i-14 and i-16 are totally neglected.
In fact there is a lot of corruption so that there is fake-files business in underdeveloped or undeveloped CDA sectors like I-14 and e12. Some investors have lost their money in i-14 because of fake files even though they invested with assurances from CDA and file transfer through CDA.
On the other hand in societies like JKCHS and multi professional so far there is not even a single case of such fraud. When you buy a plot the transfer is done at the society office in 1 day and transfer charges are very reasonable - there is no chance of fraud and everything is okey-dokey. Tension-free. On the other hand in CDA, there are high transfer charges and the process is complicated - yet no security from fraud.
Finally, if you invest in an undeveloped private society the chances are that your file will become a plot in the next 4-5 years if not sooner. In some CDA sectors you may become a grandfather and still sitting on a file - a very expensive piece of paper.