I am sorry to say, but imagine there is a problem with a store on j3 and a court is asking me if the webagency did the standard to prevent damages. then I would say that the webagency did by far not the best to protect their customer, because they used a version which is only supported for 6 months as basic for an ecommerce system. Be aware after the 6 months the version is obsolete. Most webshops need a year to reach the regular business.
That is the real reason. We started with j3 and it is full of flaws. We had to replace JText, JInput, checkToken and so on. A lot stuff which was running on j3.1 is not running on j3.2 anylonger. In our case it is not simple to create a version running on j2.5 and j3.x.
For an ecommerce system we need long term supported, secure, stable and reliable systems. We hope of course that j3.5 will have this attributes, but all STR of joomla do not by definition.