I had a feeling we were playing as an impostor, was a bit lazy story writing for Kojima standards anyway and was annoyed at it at the start. I always wanted to see how Big Boss's transition went, and thought this game would deliver that but turns out it's not even the real BB that Solid Snake fought in the earlier games. But after a bit of contemplation i seen some positives from this story; this leaves the door open for more MGS games as they can do some games on the real BB and what he's been doing (supposedly building a real outer haven), secondly i always thought it was weird how Solid Snake managed to beat the legendary BB twice, but turns out he beats his phantom.
As for the gameplay itself, like others have mentioned it did not fulfill its early potential, the game play, graphics and concept of the mother base are very good ideas they should have developed on. Maybe MGS is not meant for an open world environment as all previous games have had a linear format and there was nothing wrong with that. The second half missions as you have mentioned were disjointed and repeating missions looks like pure laziness, even the repetitive side ops smacks of laziness.
We all know Kojima's relationship with Konami soured at the end, maybe by producing this bit part game was his way of getting back at them, the story and missions felt like a half hearted attempt, the repeat missions in the second half makes it look like they couldn't be bothered with any more new content so just recycled old missions.
Nevertheless i have got a lot of hours out of this game and have enjoyed parts of it, but as a Metal Gear head i'm disappointed. Not bad for a Konami money grab over the year, 25 for GZ and 40 for this.