The NFC chip I want still doesn't exist: a CPU and flash I can write a program for, directly, no VMs, no Java, without an NDA'd datasheet. These exist, but they're all behind NDAs and you're not allowed to have them. They're used for e.g. EMV.
I saw an NFC chip that has 512 bytes of eeprom. Talks to a micro via I2C and has an interrupt that can be used to wake it up. I think it's a M24LR04E. Costs like $0.50. I think these could be useful for devices where you have a limited amount of data you want to read or transfer. Like why have bluetooth and all the crap that entails when all you want to do is configure a device once. Advantage of a separate IC is you…
More generally what I'm seeking is something in the card form factor which is suitable to store cryptographic secrets (i.e., a smartcard).
Separate IC is a disadvantage here since it creates a vulnerable security boundary and makes it infeasible to integrate the chip into a thin card.