Since I personally don't really care much about PLD I haven't compared af2/allagan for it but this is in general for all jobs.

Check and compare the allagan and mythology counterpart as some pieces are the EXACT stats as mythology so they would "technically be a waste of myth points"; example allagan hands and legs are the exact stats as af2 for warrior, so you may want to upgrade mythology pieces around those and farm content in the hopes that they drop. I believe BLM boots and allagan casting boots are exact stats too? (someone else can confirm etc idc) but just saying.