I actually love that section, and can comfortably say that, after three playthroughs, it's now one of my favorite parts of the game. I LOVE the first part of it where they take away your weapons. It's awesome to feel vulnerable again after getting to a point in the game where you have more ammo than you're ever going to need, and it makes finding a weapon or reaching a new save room a relief again. Also, it's probably the most open part of the game. You can explore the different floors in any order you please after reaching a certain point, which is great. The only part of it that sucks is that you have to rely heavily on the machine gun for awhile, and it's a pretty garbage weapon for everything except maybe the four-legged Molded.
Also, I really didn't think the Mines were THAT bad. The way people talk about it, you'd think you were going to be fighting through hordes of Molded for hours on end, but the whole thing lasts, like, 20 minutes, tops? There really aren't THAT many enemies either, and it felt earned for the game to become a bit more action-oriented. It's the build-up to the finale, after all. The Mines are short and linear, true, but they aren't all that bad or tedious, and I personally found it fun and carthatic to just go crazy with all the ammo I had at that point. The only part of the game I think is truly shitty is the final boss fight, which is an absolute joke, and probably the worst final boss (if you can even call it that) of the main series.