I sure wish inventory systems like this had gone out with the 1980's. I mean, I've seen worse this century (the original Mass Effect), but not many. The "each single widget fits in an interchangeable box, which you have X number of" thing CAN still work (Dragon Quest continues, against all odds, to do a pretty solid job with it), but I don't think it works very well with the sheer size and scope of items you pick up in a game like this.
It's -- at least hypothetically -- cool that there's such a wide variety of weapons for most characters, lending themselves to different play styles. In practice, though, I've done enough exploring and questing that I'm way out ahead of the difficulty curve and it doesn't really matter what I've got on my guys anymore. Weapons pile up, and while the equip screen has an easy way of comparing a new weapon's stats to the weapon you've already got, the Sell screen does not, so unless you just shrug and go "Okay, I'm going to sell every weapon that isn't currently equipped" it can take a long time to compare all the different shit you've picked up and what's worth keeping.
Crystals and drops are really the things that start to pile up and inhibit your actual progress; it doesn't take too long before you find yourself wanting to regularly sell or refine a few pages of them at a time.
And on refinement: I've done a bit more of it, I guess I've gotten some good gems out of it, but by and large it still feels like a pointless time sink. I've learned a few strategies (try and get to where your mix only has one or two attributes), but the actual minigame still feels like a mostly random mess. When am I supposed to hammer A? When am I supposed to tap it? Why does it sometimes go from red to green, and what do I do to get it back to red? Granted, it's been awhile since I read the tutorials, but I don't remember them being very clear on all this stuff. (And again, gems are a little on the inconsequential side when you're 5 levels above all the random monsters you're seeing.)
But mainly, the game just has a problem in how much crap you accrue, how much more difficult it can make it to find the crap you're looking for, and how much time it can take to sort through it and whittle it back down to manageable levels.