The mission-based structure was one of my least favorite aspects of Peace Walker. Before that (and ignoring Portable Ops, as one should), the games did a pretty good job at linking the world and the story in a meaningful way. Metal Gear Solid and Metal Gear Solid 2 are among my favorite games, and the fact that they packed so much content into such small areas was a large part of that. The Metroidvania-esque backtracking elements, minor though they were in the first game (and definitely pumped up with the struts' circular layout in the second), helped it feel like a place, not just a series of challenges.
I don't doubt that The Phantom Pain will be good. I loved Ground Zeroes, and if this game builds on what that did right, there's no room for the end result to be remotely un-fun. But the series has been moving farther and farther away from the structure that made the earlier games in the series classics, and it's been doing so for some time now. Peace Walker with its separate levels and missions, MGS4 with its acts... even MGS3 is rather averse to letting you revisit locations, instead pushing you forward to new areas.
One aspect of the game they've really talked up, and in fact a large part of the reason they're structuring it like this at all, is the fact that you can approach a base from any side, and infiltrate it however you want. That amount of freedom is certainly not a bad thing, but I don't feel like it's very Metal Gear. The corollary to this design is that it actively limits how tightly an area can be designed. Things like the Vulcan Raven fight from MGS1, the E.E. rescue in MGS2, and the Raikov disguise part in MGS3 are some of the more memorable pieces of gameplay from the franchise, and they simply don't make sense with this structure.
If they can still manage the sorts of setpiece-driven gameplay that made this series so special in the first place, the genuinely unique boss fights (NOT just waves of helicopters and soldiers like Peace Walker), the carefully- and deliberately-placed enemies, and the overall design style of "every moment should be memorable in some way", so that players can talk to each other and say things like "remember the part where you X", I will be happy to eat my words. But I would hate to have memorable moments sacrificed in the name of freedom; if I wanted freedom to the detriment of cohesion, I would be playing The Elder Scrolls instead of Metal Gear.
P.S. Thanks
P.P.S. But seriously, even if this game doesn't end up feeling remotely like Metal Gear, it still looks like it'll be good in its own way, and I'm still hella pumped.