I think it's worth investing your time into. It's probably the benchmark standard in terms of open-world games. If you look at something like Grand Theft Auto V, the structure amounts to "go to this point of the map and play this level". And that's really what it is - a series of levels that are connected together by the game world.
On the other hand, The Phantom Pain amounts to "here's your objective" and it rralky gives you the freedom to carry it out however you want. There's an early mission where you're tasked with rescuing a Soviet engineer. You have a general idea of where he is, but it's up to you to find him and figure out how to extract him. There's three different ways into the compound, and multiple routes throughout it. You get about four different ways of extracting him, and then there's additional objectives to complete. The game doesn't tell you any of this; it just lets you find out through experimentation. The AI are very intelligent; they're well-armed and armoured, employ tactics to flank you and flush you out, and adapt to your tactics over time. And if you consider each compound to be a "level", then almost all of them are very well-designed.
Probably the best thing about the game is the way it balances risk against reward. You can never ger completely comfortable with staying in one position, but you can never be absolutely sure about moving forward, and so you need to plan ahead and be ready to adapt. It gets to the point where single missions become complex multi-stage infiltrations and exfiltrations, and can be more fun than entire games. Even if there are issues with the story, the game works best when you're inventing your own stories and your own adventures.