Quite possibly part of this decision is based on the available resources
phonegap - develop a fit for purpose app once for all devices: development time = x hours, expertise in 1 development method
native apps - develop multiple slightly better apps individually for wach device: development time = x hours * number of devices developed for, expertise in multiple device development tools required.
So to develop for android, iOS and Windows mobile would need (roughly - I don't know how much overlap there would be, presumably some) 3 times the developer time and expertise in 3 different technologies. As commented on another (unrelated) post recently, though, this is all Open Source and if someone with that expertise wants to take on the development and maintenance of these apps...