Other downsides that show up with repeated plays are:
The unskippable cutscenes, which really become apparent in speedruns and when you get good at it and just hammer through the game. It begins to feel like a metal gear game with the gameplay and cut scene ratio
The lengthy non action story sequences - prison, orphanage, house exploration as kids, start of marooned. Anything with mandated walking.
Other than that, top notch all the way through