I'm not sure I get the problem with having multiple weapons to fight multiple things. I like that idea. A good fighter SHOULD have a decent weapon of each type (bludgeoning, slashing, piercing). Heck, that holds true even in 3.0 games.
I nearly splatted my 15th level party with a six-pack of clay golems -- they spent three rounds fighting before realizing that the cleric was the only one with a blunt magical weapon, and therefore the only one hurting it. The first thing they did when they got back to town was buy back the +1 warhammer and +2 greatclub they'd liquidated as useless...
As for specialty materials -- like silver or adamantine -- the whole "Only DR 10" deal is pretty much gonna make that less of a hassle. If you fight werewolves all the time in your game, you'll end up with a silver longsword at some point. And if you fight fey, you'll end up with a cold iron rapier at the very least...