Replacing 14/2 wire with larger gauge (12/3), is this a problem?
You're good to go. You could run #10, #8 or #6 if you wanted (of course you'd have a heck of a time terminating it in the box, but that's another story).
You're always free to run a larger gauge wire since, as you know, it can handle the higher amps.
Make sure you label the circuit (as others very properly noted) to remind yourself and future electricians that this is a 15a circuit with some #12 wiring and that it's not #12 all the way to the breaker.