As I've only played Path Of Radiance and Radiant Dawn (I played a couple minutes of Sacred Stones, I might eventually get to it), there are some things that I loved about those, which probably aren't a common thing in the franchise, but I'm missing those a lot. The Laguz were really great,and Taguel/Manaketes here just don't really compare for me. I liked that the Laguz had a set meter in which they could transform, and were otherwise weakened, so you had to plan around that and have more interesting strategies.
Another thing I loved about the Laguz was about how much variety there was. There were a lot of different types, and even among the units of each unit, there was a greater degree of variety.
The Dragonstones/Beaststones are different, not necessarily bad or anything, but I just don't like this system nearly as much.
Tying into that last point, it would've been nice if class changes could have been reflected in the character portraits as well, as they were in Path of Radiance/Radiant Dawn. But again, I know that there would've had to have been a lot more work for this.