You step out from the darkness behind a guard, and stab him he is surprised & flat footed.
Your get in an argument with a scary dude you both go for your blades, your initiative is higher than his, fair enough you catch him flat footed as he can not properly defend himself.
You face off against 6 guards in a long large, room (can't cover in one round), and you’re telling me that you run across the room, roll initiative and even though you’re all aware of each other prepared for the fight that you still could catch them flat-footed!!!!
And this then is one of the key places where the GM has to step in and adjudicate things. The major factors to look at here are encounter distance
. Encounter distance is the distance at which characters can check for awarness of the other side, if they are aware then they can choose to go into initative and start combat.
In your third example the encounter distance is set at some distance too large to cover in one round (lets say ... 100'). Both sides check for awarness and everybody sees everybody else. Both sides decide to go into initative (obviously they recognize each other as enemies). Since everybody takes their first action standing 100' away nobody will be flat-footed by the time melee begins (though maybe some ranged attacks could come into play ...)
But lets say that you have your encounter start at 100' as before but the guards don't recognize the PC's as enemies and the PC's decide to try some subtrfuge before violence (suprising I know :wink: ) they want to walk over and chat up the guards then attack. The important thing here is that you do not roll initative untill combat starts, so nobody roll initative and everybody is flat-footed. The PC's stroll over and when they finally are ready to attack it will look more like your second example with both guys going for their blades and both sides rolling init .... maybe if the players do a good job of roleplaying fast talking the guards you could award them a +2 circumstance bonus to init. Maybe if they did a really good job, maybe threw in a few bluff/diplomacy checks, then you could award them an entire suprise round.
However, now lets say the where the PC's enter the room it is dark. So the PC's are 100' away and aware of the guards but the guards are not aware of the PC's. The PC's decide to sneak up on the guards and attack. They roll init and become un-flat footed as soon as they take their first action. Meanwhile unless the guards become aware of the PC's sneaking up on them (spot/listen vs hide/move silent) they will not roll initative and remain flatfooted. When the PC's are finally ready to strike it looks like your first example, they jump out of the shadows and take a suprise round. If they should also win init then the guards will continue to be flat footed durring the first round and that will probably spell their doom.
Thing is, this is the sort of thing that is very dependent on the situation, as a GM it is exactly your job to play it by ear and try to make sure that the game runs smoothly while remaining as close to the rules as possible. The thing to remember is that there is no "preparing for combat". Preparing for combat is what you do on that first round when you are becomming un-flat footed. The way to make sure that you are "prepared for combat" is to make sure that you become aware of your enemy (*cough* send a scout *cough*) when you are far enough away that you can drop into initative and become un-flat footed before he closes to striking range. Of course if he sees you draw steel and buckle on your sheild he will do the same thing.... If you want to catch your enemy flat footed you either need to play it cool and trust that you are the faster draw or else sneak up on him.
Hope that helps.