Many have seen episode 51 of Metal Gear Solid V: The Phantom Pain, and the fact that it was cut made them think that the game was not finished.

Kenji Yano, who is a well known expert on the series who wrote multiple books on it, and appeared with Hideo Kojima in his broadcasts, including the latest HideoTube, weighed on this possibility on Famitsu, arguing that the game isn't unfinished, but it ended exactly as Hideo Kojima wanted.

Keep in mind that what you'll read below includes heavy  story spoilers, so you should probably head back if you haven't played the game yet.

First of all, Yano-san explained the reasons why some players might feel unsatisfied by how The Phantom Pain was brought to its conclusion, also arguing that episode 51 isn't essential to the game:

"I think there were two stages to this. First, you had a certain number of players who finished Chapter 2 not long after the game came out and went, “What? This Snake wasn't the real Big Boss!?” It's similar to the way people reacted to MGS2 (laughs). Some players couldn't accept that there was a new main character, Raiden, and they got really angry. But now MGS2 is considered a masterpiece. MGSV is a much longer game than MGS2, so it's like its length amplified that feeling."

"Then after this, people started to see the cut Episode 51, The Kingdom of the Flies, which was included on the bonus disc but posted online, and then reaction changed to people asking why this wasn't in the game. In other words, the story arc with Eli being unresolved made people feel the game was incomplete. But personally, I don't think the Kingdom of the Flies episode is essential to the game."

Yano-san then elaborated on the sudden switch after episode 46, explaining that the outcome is exactly what Hideo Kojima wanted to begin with:

 "I don't think its absence is the direct cause of this reaction. Up until Episode 46, The Man Who Sold the World, players experience the story as Snake, but then they suddenly have the rug pulled out from under them. They find out that they themselves were Big Boss. Then it becomes their story. They themselves participated in the massacre on Mother Base, Quiet's disappearance, Huey's exile. I think The Kingdom of the Flies became an outlet for venting all the unease and confusion that followed that revelation. But really, this fits right into what Kojima-san wanted."

He also argued that many players may have felt an excessively heavy burden in experiencing themselves becoming villains:

"Kojima-san wouldn't be satisfied with having the player just think, Wow, Snake's a monster, he killed a bunch of his own men. Kojima-san has talked about “giving Snake back to the player” with MGSV, and I think this is probably the kind of thing he meant."

Yano-san then talked about Episode 43, explaining that it fits right into Kojima-san's belief that the goal of entertainment is to move the audience;

"That's quite a demand he put on the player (strained laugh). To be honest, while that episode will disturb the player, Kojima-san believes that the greatest goal of entertainment is to move the audience, and that he must make games that can do that. I believe that's why he has the player do such a thing. There's some overlap there with the final scene with The Boss in MGS3."

Personally, I don't feel that the game is unfinished. Cut content is part of any production, and doesn't really make it unfinished. Of course, we don't always get to see it, like in this case.

Your mileage may vary, but Yano-san seems quite convinced that Hideo Kojima concluded his part in the Metal Gear Solid series exactly as he wanted. His idea of the message Kojima-san wanted to convey is quite interesting:

"We can be Big Boss now. We can all hold our heads high and work to save the world - our real world. So let's do that. Why not, right? I think this is the “empty space” Kojima-san has given us through MGSV."