Neodymium has greater magnetic strength and so requires a lot less material to work in a speaker design. A speaker designed around it doesn't HAVE TO sound intrinsically different, but the relatively few examples of neo woofers DO sound different because (1) every speaker design sounds different anyway, and (2) designing a neo motor with exactly the same magnetic field as a non-neo motor that it would replace is not yet widely understood. Neo driver design is in its infancy. Some of the early concerns have had to do with neo's tendency to lose magnetic charge under lower heat than is true with ceramic, so cooling strategies had to be prioritized.
Already it's getting better for tonality and types though, if comparison between the Deltalite and DeltaliteII specs and charts are any indication. Newer drivers by BMS, Ciare, B&C - and Eminence's promising new Kappalites - finally begin to show what the potential is. Some of that is in motor design itself, some is matching it to a better suspension fit for it, and the cone and dustcap combinations. As more people demand lightweight neo, more R&D is put into good neo drivers for various applications.