I think it really is. For example, FF XII has a drastic fall of quality mid-game, it`s like two separate games that uses the same assets at some points and try to somehow connect each other, the game start great but the storyline becomes extremely shallow and all the characters became a shadow of their former-selves, some almost don`t have dialogue even. And we all know Sakaguchi left S-E in the mid of development cycle of this game.

MGS V, even i haven`t played it yet, many people say the game endings way to abruptly, when all MGS games have a closed history and fitting ends, because all of them were "the last MGS game" when released so they left little for sequels and had to rebuilt themselves plot wise from the ground each new installment ( wich actually made the storytelling of the franchise be extremely good).

FF XV is getting the same kind of critiques, the game even being really good it`s has a feeling of inconsistency in it, be it how the story is paced or how the open world works.

It was Yasumi Matsuno who left during FFXII's development, not Sakaguchi. But I agree with you. Somehow, you can feel where he was involved and where he wasn't.

But then again, Super Metroid almost got canceled three times during development because the team couldn't decide on how the game should look and feel. In the end, though, it's one of the greatest games ever and everything blends together perfectly. So ultimately, it can't be perceived every time.

Disaster: Day of Crisis had the same thing with parts of the game.

I'd say yes, but cant agree on your example. I think FFXII is steadily good from beginning to end. In fact I think from mid point forward it gets better. I think it could be said about FFXV.
Usually games that take very long (like FFXV) have a lot of ideas put onto them and most of them scrapped, yet aspects of them still make the final game. So you get a convoluted game with good ideas but none of them live to their full potential... Just like FFXV.

Well, we have to agree to disagree here. I think it`s very common to see games that start fine in a set rhythm and pace and then suddenly the game start to rush the ending. It`s very common in movies and games for this to happen, it looks like they say "hey, we had one year to finish the game/movie and we still have to test and etc and we only made 50% of it and we only got 3 months left!" and they run to meet the schedule. 

I know games and movies aren`t made linearly, but it is a feeling I have in many movies and games nowadays, the games/movie paces suddenly changes and The End and that some good 30 min of movie were cutted or some hours of gameplay. I would consider this convoluted development.

I would say no, because that would usually result in the whole game being bad rather than a sudden drop in quality or something like that.. :/

Windwaker seems to be missing some dungeons at the end and Uncharted 3's story doesn't fit around the set pieces all that well, so even the best get inconsistent. Software development is convoluted by nature.
Better is to spot the few games that turn out consistent from start to finish. Erm, Tetris!