Being on a codeshare is a severe disadvantage when push comes to shove. The operating airline can/will do nothing for you, and the codeshare airline often has little presence or ability to do something. The alliances help this situation somewhat, but in your scenario the only value of a codeshare is to give revenue to airline X instead of Y (and Y operating the flight knows you took their revenue away, by choice). In theory codeshares increase total revenue, but in practice a few airline employees view it as taking bread out of their mouths. I try to avoid codeshares unless there is a good reason.