This looks attractive, but does not /really/ help: the reason people use Cydia is not to get apps, but is instead to download "extensions". It is not possible to install these modifications (things "be able to put five icons on the dock instead of the default four") on any of the modern mobile platforms without first jailbreaking: the ability to "side load" an app is honestly kind of boring.
That specific customization is possible but requires you to replace that entire component, so it isn't really a customization any more than saying you can customize that particular thing by just replacing the entire phone. ;P
This distinction becomes important when you want to install that customization on a device for which the stock launcher is not open source but has been customized to fit with other apps, or simply when you want multiple customizations from different people.
However, if you insist on something a little more concrete: what if you want to add new buttons to the Android notification center, add new features to the status bar, or affect the behavior of the lock screen? These are not apps you can replace.
- a carefully groomed, public facing store monitored by apple (they have already)
- allow other app stores for non-monopolistic competition (eg: Amazon's android store)
- allow developers to use DRM on their apps
- allow app files to be loaded manually by the user