We theoretically investigated acoustic phonon spectrum and group velocities in an ultra-thin layer of wurtzite GaN embedded within two AlN cladding layers. The core GaN layer thickness has been chosen on the order of the room-temperature dominant phonon wavelength so that the phonon spectrum in such a structure is strongly modified compared to bulk. We derived equations of motion for different phonon polarizations in the anisotropic medium approximation, which allowed us to include specifics of the wurtzite lattice. Based on our model we calculated phonon density of states and phonon group velocity. Using several other example material systems, it has also been demonstrated that the phonon group velocity in the core layer can be made higher or lower than that in corresponding bulk material by a proper selection of the cladding material and its thickness. Presented results shed new light on the effect of barrier material on the phonon spectrum of heterostructures and can be used for modeling the thermal and electrical properties of such structures.