According to former Naughty Dog designer Benson Russell, who worked on both installments and Uncharted 4: A Thief’s End, the situation in production changed. During the first game, the team was smaller, and Neil Druckmann’s decisions went through other leads, which caused some ideas to be rejected.
In the case of the sequel, the studio had grown, and there was less such oversight. As a result, according to this account, Druckmann received complete freedom and "did whatever he wanted with the project." This is linked both to the high review scores and to the criticism of the game.
It is also noted that the director faced resistance on the first game, but not to the same extent on the second. The situation is compared to the "George Lucas effect," similarly to Gabe Newell and Todd Howard.