Browsers are limited to using the built-in webkit engine, many default applications are fixed to Apple applications and can not be replaced as the default by a 3rd party app, apps can only be installed from the Apple App Store, support for PWAs is poor, and the UI/UX doesn't provide good discoverability of functionality (This seems to affect most Apple products but for some reason people here seem to think Apple has great user interfaces. For the worse example of this see tvOS.).

Also when switching providers iOS has a habit of sometimes getting into a state where it will refuse to send SMS or MMS messages. This has plagued it over many versions with the only resolution being to wipe the device and not restoring any backups because restoring will then break the functionality again. I know several people who have been hit by this and the support forums are filled with this happening to people.

The latest news is that since version 6 receiving certain email can lead to your phone being compromised even if you don't open the email. Which reminds me of another point. Despite Apple's best efforts there still exists software and/or devices available to governments which can subvert the security protections on iPhones. Also don't forget that time when receiving certain text messages could lock up iPhones.

That is just a short list of a few of the ways iOS is not great. You can argue it is better than some other systems but that still doesn't make it great.