From a technical perspective, 3rd party apps are written in a completely different framework than 1st party apps. 3rd party apps for the most part run under managed code (C#) which in general is less performant than native code (C++) which is what 1st party apps are written in. 3rd party apps also have less access to certain capabilities of the OS, since the public SDK doesn’t have the relevant APIs exposed.
However this is starting to change. Some 1st party apps are being written in managed code, using the same, new developer SDK that is provided publically (the one that unifies Windows desktop and Windows Phone development). Apps like Calendar, Music, and Video are written in this new framework. But it’s also why those apps (the music and video ones in particular) kind of suck.
UX wise, it’s totally the developer being lazy or unfamiliar with how to make a good design for WP.