Personally, I feel like Drake's Fortune is the outlier of the franchise. It's still a solid game in its own right, but compared to the rest of the franchise, it feels somewhat generic, and both the narrative and characters don't feel as developed as they could be (I'm looking at you, Roman and Navarro).
Granted, Drake's Fortune was an entirely new IP, with Naughty Dog likely not knowing where the franchise would go. And I'm not hating on the game for what it is. As previously mentioned, it's still a good game that is just overshadowed by it's superior sequels.
I personally feel like a remake of Drake's Fortune would be the best way to carry the franchise forward.
• It's a perfect way to bring back the main cast without interfering with the ending of A Thief's End.
• The narrative can be better refined, bringing the story more in line with the rest of the franchise.
• The antagonists can be better developed and utilized. Eddy was fine (though I'd still love to see more of him). Roman and Navarro were forgettable, and the twist didn't work as Navarro had virtually no development until it occured.
• The environments could be expanded upon. The jetski sections in the flooded city could be more open and explorable, similar to the Madagascar section of UC4, or Western Ghats from LL. The primative traps left by The Descendants could be more prevalent, acting as obstacles, traps for both the player and enemies, and better foreshadowing their presence.
• Some other gameplay refinements such as better gunplay, movement, dynamic environments would also help elevate the game closer to its sequels.
• Inclusion of multiplayer, because Uncharted's multiplayer has always been criminally underrated.
It's worth noting, I also wouldn't pass up on the idea of more spinoff titles with Chloe, Sam, or even Cutter.