Even though the core architecture remains the same for both xenapp and presentation server they had introduced some new concepts and feature in xenapp.
1. Moved many configuration items from citrix advanced configuration tab to citrix policies and stream lined it like Microsoft GPO.
2. Added many HDX policies to support multimedia
3. Introduced VM hosted application which works with xendesktop
4. Added windows 7 user experience to published desktops
5. Added worker group concept
6. Increased security features linked with Microsoft UAC & Microsoft RDS
7. Added VM provisioning feature via provisioning server