I agree about the D1 Mini being nice. I think it's way better than the Uno style D1. The regular D1 is pretty much the same thing only 4x bigger and with the idiotic Uno off grid header. The only real reason to use the regular D1 is for shield compatibility but there might be issues with the 3.3V I/O, I'm not sure there's some confusing information on whether the ESP8266 is 5V tolerant or not. I own both but the only reason I bought the regular D1 is because it was falsely advertised as being a shield.
That said, the D1 Mini is not really intended for use running the AT firmware to communicate with a regular Arduino. You could do it but there's not much point in all the USB stuff on there if you're not programming it directly.