I think it's a mix. Kojima was pretty clear that he wanted to make MGSV about the player creating their own stories and de-emphasizing an explicit plot. The op

I think it's a mix. Kojima was pretty clear that he wanted to make MGSV about the player creating their own stories and de-emphasizing an explicit plot. The opening is meant to be a bridge with the older games, hence it having a structure more similar to them (and specifically to MGS4). But on the other hand I got the impression that the game was definitely not finished plot wise and even stylistically, at least not to the point that Kojima and his core team had originally envisioned. It felt like we got 90%, but that last 10% was the bit that was supposed to fill in the gaps in the plot and leave the player feeling satisfied. Compared to e.g. the ending of MGS4 (which is my favorite in the series), the latter third of MGSV was just so... unfulfilling. I suspect friction over Kojima's vision versus Konami wanting to get the game to market was why they parted ways, even though Konami was very clearly killing the golden goose.