There is a lot of older stuff in the metaphysics literature (Black, Adams, etc.) and a lot of more recent work in the philosophy of physics literature (Saunders, Ladyman, French and Krause, etc.) and the two discussions don't have a lot of points of contact. (Disclaimer: I'm going to read Katherine Hawley's paper on the PII in the next week or so; perhaps this will join the two debates together a bit more for me.)
Here are a few things I find confusing. (1) The physics people often seem to run together (sometimes on purpose) epistemological issues about indiscernibility with metaphysical ones. The fact that two particles are indistinguishable for us seems to entail, to some, that they are indistinguishable simpliciter. I'm not clear on what, if any, metaphysical lessons can be learned when we take this sort of strong empiricist stance. (2) Haecceitism is often not well enough defined. Sometimes it means that objects have primitive thisnesses (following Adams) but sometimes it just means objects are (or could be) primitively different. This is an important distinction. The more minimal kind of haecceitism, which I'd argue doesn't even deserve the name, just says we can have objects that are perfect duplicates but nevertheless differ. They don't differ because they have special thisnesses, because they don't have thisnesses. They just differ even without differing in their (non-identity-based) properties. (3) Saunders and others want to sidestep the PII by denying that bosons are objects. They are some other sort of entity. But how does this supposed to help with anything metaphysically interesting? I always took the PII to apply to things of any sort.
Finally, a note: physicists often make claims about particles being identical when they really mean they are of the same kind. Argh!