I came into Jak and Daxter last year I think (might have been the year before that), so when I talk about the games there is no nostalgia talking.
When I sit back and compare it to Uncharted and think about weather I would prefer a Jak 4 or Uncharted 4 I always lean towards Jak 4. Uncharted's strong point seemed to be on those large scale events like the burning house, airplane crash, train wreck, ship flipping and so on… It also has some great humor too. The game is very linear, and unless they are ready to open up the world in Uncharted 4 I will not be voting for that one.
Jak and Daxter has the humor alright, but it also has original and engaging story and characters. Uncharted's characters can be compared to characters in many other games, whereas Vin, Daxter, Samos, Torn, Praxis, and Errol just seem like people I've never met before. The Jak world is easily larger and way more full of life than Uncharted. I like the whole mystery around the universe and precursors. The fact that there may or may not be these all powerful gods controlling the world in secret, or not for the first 3 games (2.8 anyway).
Jak's world is more unique and special, like Rayman's haunted fairytale world from Rayman 2 and 3. But the great thing is that no one truly even knows what lies beyond Haven City and the Wasteland, let alone the universe. Jak 3 let the games have a good long break which a semi-conclusive game. It felt like the end of a really long series of events, but it also felt like they were not finished, just ready to take a little break.
ND could revive Jak and Daxter if they tried to lean more towards cartoony than realistic, and kept the universe mostly in tact.
Uncharted doesn't seem as unexplored and full of uniqueness though. It's just our world, earth and some guy that wants to find a few secrets here and there. Sort of just 'The Mythological Myth Busters Who Get Followed by Some Mean Spirited People"