I was like most people on this forum who found it annoying that suddenly Apple's latest iOS upgrade caused such issues with my POP mail. I have also sent Apple a feedback as per recommendations in this forum.
I've now been making changes to my POP mail accounts (on my Macbook and desktop PC using Outlook) so that emails now only get deleted from the server when I remove them from the Deleted folder on those devices. This way I can still have access to them on my iPad. Basically I've had to rethink how I deal with POP mail since the iOS 9 changes to Mail. I am now finding this to be preferable to how it used to be pre-iOS 9. Let me explain.
Prior to iOS 9 the memory usage of my POP mail accounts on my iPad would just continue to grow and eventually I had to remove the account and then add it again to get the usage back to low MB figures. I found this very annoying.
In recent years it has become apparent that Apple is directing it's users to make better use of the cloud when storing documents etc. Apple does not provide large memory on it's devices, such as iPads. The latest iPads max out at 128GB but really we only need around 32GB if we are using the cloud to it's fullest potential i.e. storing as much as possible away from our device.
I am now starting to think that Apple have purposely designed iOS 9 so as to treat POP emails the same way i.e. keep them in the cloud (or ISP's server) and not on the iPad itself, therefore fixing the issue of the Mail app using so much memory on the iPad. I have noticed now that my Mail app stays around the 60MB size all the time and no longer increases to ridiculous sizes (close to 1GB) like it did pre iOS 9.
I am now coming around to liking this new arrangement. Apple has a history of making users think outside the box and look to better ways to manage their devices and memory usage (e.g. they were first to remove floppy discs etc).
I have a Macbook Air as well as a Desktop PC. Both devices have my emails fully downloaded and accessible, when required. Recently (under iOS 9) if those emails are then deleted from the server then they are still accessible on the Macbook and PC but no longer on the iPad. I don't find this a problem now. I have now changed the PC Outlook settings to only delete from the server after I remove the email from the Deleted folder.
In summary, I wouldn't expect Apple to "fix" this issue too soon as I think they are simply retraining us to make better use of the cloud and email providers such as iCloud, gmail, Hotmail, Outlook.com etc which don't cause these problems of email suddenly disappearing.
At the end of the day I now have a work-around that ensures I can access all my important emails on any device (including my iPad) and at the same time keep the Mail app usage to a very low level that no longer requires me to remove email accounts in order to keep my iPad memory usage to a minimum. I'm now starting to like it.