The Jax series is the perfect example of how Naughty dog mostly follows the trend, not sets them, but does it well enough that they still really make good games.
Linear mascot platformers featuring animals are the big thing? Well lets make a bandicoot into hip mascot give him basically 2d platforming level design turned 3d. Animal mascots are out and open world platformers are a big thing now? Well lets turn crash into an almost human and give him an open world. GTA is big? Well lets take jax and put a focus on driving in the open world and also giving him guns. Covered based shooters are all the rage now? Well lets make a cover based shooter with Uncharted.
I really do love all their games and they are extremely well made, but for some people open world fun loving collectathoning is their favorite thing. 2 and 3 really are good too, but they are so different from 1, and they probably haven't aged as well as Jax 1 since the GTA and shooting genres have evolved so much, while platforming has basically been figured out ever since mario 64.
Really if anyone wants to get the general gist of the evolution of game design from the mid 90s til right now, playing every naughty dog game back to back would be one of the best ways to do it. At least they don't fall behind the trends like some companies, and they may actually be trying to set the the trends with their next game.