Here's my response to my troubled player:
Remember that being Flat-Footed at the beginning of a combat round is about how quick a character moves and reacts to a situation. It's based on DEX. It doesn't have anything to do with awareness of enemies (which would base it on WIS or INT). That would be Surprise. One rule I read said that Surprised characters are flat-footed because they haven't acted yet in a round, not because they are surprised.
What I want to bring to your attention is the Feint Combat maneuver.
Now, this is something that can be done on a character's action, during a fight.
So, let's say Caelis and Thrallan are going at it, and on the third combat round, Thrallan decides to attempt a Feint. What he does is give up an attack (because he's acting like he'll attack in one direction, but pulls that attack in order to fake out his enemy). You don't get an extra attack to pull off this maneuver, so it takes two attacks to do it--the first is your feint and the second is your real attack.
Mechanically, Thrallan rolls his Bluff skill instead of his usual attack when he feints. Caelis gets a free action to fall for it or not by rolling his Sense Motive skill. If Caels wins, Thrallan's feint fails, and combat goes on as normal. The net result is that Thrallan gave up an attack to try.
But, if Thrallan wins the Bluff vs. Sense Motive toss, Thrallan successfully confuses Caelis with his thrust, then comes in from another direction. If Thrallan's feint succeeds, Caelis is considered flat-footed (can't dodge or parry Thrallan's next attack) until just before his next turn on the next round. Thus, Thrallan feints in round 3 and then attacks flat-footed Caelis on round 4.
Now, logically, if a character can be considered flat-footed that quickly, right in the middle of a combat, is it a stretch to consider that a character can be considered flat-footed, the victim of the first blow from his enemy?
What happened with the feint? Thrallan faked a jab to the right, then pulled his swing. Caelis fell for the ruse, adjusted his stance to defend the blow coming in from the right, when Thrallan quickly shifted and struck into Caelis' exposed left--all in a matter of seconds.
If getting the first attack in is an advantage (and I know it is because, in the few fights I've been in during my life, I've been punched in the nose before I could strike, my eyes watered, and my opponent remained at an advanted during the entire fight), as I think all three of us will agree, I don't see it as too far a stretch to say that being flat-footed because your enemy struck first is akin to being victim of a feint.
Your opponent struck fast, and even though you were quite aware and ready to defend yourself, your opponent got in the first blow and took the advantage.
If you survive that first blow, your opponent's advantage is not as strong (you are no longer flat-footed), and the fight ensues.
But, as it says in the game, "striking first can mean the difference between life and death," the game designers chose to implement that first strike advantage with the flat-footed rule.
No game is perfect, but I think if you really consider what is being described here, you might find the flat-footed rule a bit easier to swallow.
