I've been away at Yosemite for a few days but just finished the read-through of this thread.
I'm glad to hear Karen (the superintendent) and Mark (the chief LE ranger) replied quickly, Adam... I hadn't seen rock-throwing incidents where you were describing them, but that is very frustrating. Hopefully the signs will do some good. With eroded funding on top of the sequester effects, we're down to 3 law enforcement rangers for the whole park, so I think it has been difficult to get folks on trail with any frequency.
In regards to the original question: I've noticed higher visitation pressure over the last few years, though I'm not sure it has been especially significant since NP status in January. I've noticed an increasing amount of trash on and near trails over the past several years, as well as more trail short-cutting, graffiti on rocks and trees, and more dogs on trail (which aren't allowed beyond paved areas, in case folks aren't aware). I've organized a few trash clean-up events for all staff and have tried to push for a more responsive attitude in dealing with trash and graffiti, but it can be hard to stay on top of it, especially as increased visitation is likely to continue.