As much as I can sometimes find playing with customization fun, my favorite progression system is still the classic system of FFIV and many other traditional JRPGs of its era. Specifically, that each character has a set class, rather than malleable jobs and acquire skills at level up rather than by some other means. One of the reasons I like this is it puts more on level growth than just stats which makes level grinding more fun. Another is it's too easy to get carbon copy type characters when you can make them anyway you want, so I prefer at least some rigid structure to each character. Something in between would probably also be pretty nice to me where characters have some choice of class/job but those choices are limited and vary among characters. The closest example I can think of is Seiken Densetsu 3, but that's not a good example to me, because I don't like that game. Another example I like is Breath of Fire 3 and 4 where there are level based skills but also customization of both skill and stat growth through the master system. FFIX is a pretty good example too. It doesn't tie skill growth to levels, but at least many of the skills and equipment are unique to characters. The sphere grid system of FFX starts out alright in a way that almost has set, but somewhat flexible classes, but kind of goes offrails near the end when the grid opens up more.