Apple store is still accepting hybrid apps.
From my experience your app will be rejected if you use server side code to generate your page layout. But if you use PHP/MySQL back end as a web service to communicate with a mobile client then you are good to go. This is a rather bed situation because you need to use your hybrid app for page content generation. But at least your app will be accepted.
One more thing your app layout must resemble native iOS apps.
Titanium is still a safe bet because its final result is a native app. In case of Phonegap a good solution is Phonegap + jQuery Mobile or Phonegap + KendoUI (probably the best solution because it UI is closest to native iOS look).
EDIT :
For better clarification:
PHP/MySQL back end as a web service
All your pages are already inside phonegap app (in assets/www dir) and ajax is used to communicate with web server and retrieve content (for example news lists or single article data). Then that data is used to generate a page content inside a html file.
Also take a look at my answer (to a similar question): https://stackoverflow.com/a/14166593/1848600
Phonegap and loading a web app from remote server
Basicaly you open you remote web app and show it inside phonegap app. Here's an example (also my answer) : https://stackoverflow.com/a/13996437/1848600