The most publicised issue is that the last chapter that was completely cut from the game, but the issues with the game go much further then that. One of the hallmarks of the MGS franchise is it long dialogue and cinema like cutscenes, however MGS5 has hardly any dialogue or significant cutscenes. Towards the end of the second chapter, the game forces you to replay old missions to progress with the main story. Many scenes just feel janky and unfinished, like the car ride with skullface where you sit and stare at each other for a few minutes while the theme music plays. One of the major overarching plot points is your characters descent into becoming a "demon", yet I feel that the game really failed to convince me that any decision I made was particularly evil. If Kojima had more time, maybe he could of done a better job with that.
The best scenes are the ones that made it to the trailer, if the rest of the game could of been at that quality it would of been fantastic. Perhaps the most disappointing thing about the game is that it clearly had a lot of promise and if Kojima was given the time he needed, it could of been an amazing game.