Mobile Native Applications today can usually support higher graphic rendering and better synchronization enabling a richer experience compared to the mobile web apps, especially when it comes to games. However for many casual games, mobile content and mobile social networking, Mobile Web Apps developed in HTML5 offer a great user experience, with the advantage of being cross compatible across all smartphones (while developing native apps, requires the developer to release one or even more versions for every device).
The other downside for Mobile Native Applications is that the business frameworks and monetization tools are also different. Companies publishing web apps are free to use any online payment method they wish such as Credit Card, Paypal, Carrier Billing, etc. Instead companies publishing Native Apps will usually utilize the payment system supported by the OEM (as in the case of Apple Inc.) or utilize the payment systems supported by the store (as for the case of GooglePlay the new version of the Android Market).