I'm helping our local Fablab to manage physical access with a series of ESP8266 and esp-rfid https://github.com/esprfid/esp-rfid/ (of which I became maintainer. If you want to use it as well I can help!)
I would pay real money for a system like this with actual security. The obvious starting point would be CTAP2 — the protocol is open, high quality fobs are inexpensive (not as cheap as Mifare, though) and widely available from multiple sources, and the protocol has been analyzed for real. One could probably even extract an actual production grade implementation of the NFC side from the Android sources. Apple Home Key support would be nifty, too. PIV would be another credible choice.
Extra bonus points for support for real commercial readers using OSDP’s transparent mode or whatever they call it these days. As I understand it, an early standard involved a horrible hack that was so horrible that HID managed to patent it, but the protocol was redone to avoid being a horrible hack, and the new version is also unencumbered. Although maybe the spec costs $30.
