Dagger and Morrowind, even years later, are great games still. Oblivion was great at first, but it has not aged well with its bad character movements and poor world physics (such as everything on a table moving when you pick one item up). Skyrim is great (even if dead dragons dropping from the sky isn't), but Morrowind has the best "open" world experience because it isn't stupid big like Daggerfall, it lacks the compass markers of Oblivion, Skyrim, and ESO (which marks even non-active quests), and it is possible for people important for quest lines, including the main one, to be killed.
I would have to assume that is because MGS was never intended to be in such a world. You sneak through a small location, uncover plot elements, and encounter some very interesting and unusual characters. I imagine the results would be worse than taking Mega Man out of a side scroller and putting him in the 3D world of Mega Man Legends.