The warning-on-two rule is understandably an issue that not everyone will agree with. I happen to like the rule myself, even though I agree that one should not be required (in any sense) to warn their opponent who is about to shoot at the wrong ball.
Back in college, I was playing in an annual tournament to try to qualify to represent my school at the ACUI regionals. It was a very important tournament to me at the time.
I was on two fouls, but my opponent failed to warn me. He was an experienced enough player that I thought he knew the rule, and was wondering why he wasn't warning me. I kicked, and I fouled.
He said, "three fouls, you lose". I said, "Wha? You didn't warn me." The rule sheet was hashed over, and the tournament director was called in, even after showing the kid the rule. LOL. Suddenly I felt like I was in the Twilight Zone when the TD sided with my opponent! LOL.
I said, "it says right here in the rules which you handed out: the opponent must warn the player who's on two". He was the bowling coach and didn't really know much about 9-ball, so he gave me a bowling analogy of why the written words didn't matter.
Eventually I convinced him that the bowling situation is not an apt analogy. It's just the three foul rule and you have look at it as its own separate rule.
In the analogy to a rule requiring a seated player to warn his opponent who is aimed at the wrong ball, here is where, IMHO, the analogy breaks down: If that were to be made a rule, it would not be enforceable. What would be the punishment for breaking the rule? How would you know that the seated player even noticed? How would the seated player know for sure what the shooter is planning to do with the shot? IMHO, this rule simply wouldn't "work".
The difference in the on-two-warning rule is that it does work. Apply any of the above questions to the on-two-warning rule and they all have easy answers where applicable.
In another sense, I do agree that it's somewhat of an inconvenience for the player issuing the warning. That's why I always warn my opponent immediately after the 2nd foul rather than right before he shoots his next shot.